Heater Channels

If just one area is slightly gone and the rest of the channel is 100% solid, you'd be ok to let in a proper repair (e.g. if it just needs the bottom panel that bolts to the floor replacing) otherwise it's best to replace the whole thing in one go. don't bother with the cover up panels as they're just covering up existing rust and storing problems for later.

Strip Down

Battery - regardless of which side you are working on
You should remove the following on the side you are doing:
Front and rear wings
Front and rear bumpers (to enable wing removal)
Running board
Carpet
Seats - back and front but leave the rear seat cross brace in
Rear side panels
Also check carefully for the main wiring loom and any other wires or pipes (it's not necessary to remove the main wiring loom - it can be pushed out of the way safely).
Door
Finally, either pop the windows out or cover them with card taped in place to avoid weld splatter on the glass.

Bracing

Before you do anything , measure twice & make sure the shell hasn't sagged over the years
This is the most important step to doing the job properly. There are those who argue it's not necessary, but as far as I'm concerned it's not worth the risk and hassle for the sake of 5 mins work. Weld bracing (angle iron will do fine) into the shell before any metal is cut out. You need to brace the shell to keep everything in place and the door gaps etc correct (you wouldn't want to weld it up to find the door won't fit do you)
I usually brace the following as can be seen in the pics below:
A to B post, A post to A post, B post to B post
If you weld these in in areas usually hidden by front carpets or headliners it cuts down on the clean up work afterwards.
I also leave the rear seat base crossbar in as an added strengthener. Some of the pics show the heater channel missing but they are mid job & are to illustrate where the bracing goes only.

Now undo the 13mm body to chassis bolts down the side you are doing and from the rear corner to the centre of the tunnel at the rear (where the chassis number is stamped). most of these in the channel will probably snap or just turn and not undo. If the channels a real rotter, leave them be and you can attack them from the inside when the bulk of the channel is out. alternatively, cut the heads off them from underneath.

Which way you cut out the bulk of the channel doesn't really matter, as long as you are careful and don't cut off the bottom of the A or B pillars (if there are any!) as these are a useful reference for ligning up the channel. If it's welded to the floorpan (common 'get through the mot' welding), make a vertical cut through this first, being careful not to damage the edge of the floorpan (unless you are replacing that too). When cutting the front, if your A post seam to front wing area is sound only cut up to the area under the front wing join, otherwise cut up to the A post seam, but not through it unless it's rotten and is going to be replaced. 
The front of the channel is attached to the bulkhead, so unless yours is as rotten as the last starting point picture above you'll need to cut around the channel to free it. If it is that rotten it will probably just pull out. You can now cut off the tops of the floorpan bolts if there's any poking through.

When cutting the channel out of the back area, make sure you leave in the strengthening bit  by the seatbelt mount as shown in pic 3 below. If youre replacing the rear door - wing panel, cut off the bottom of this now as it will allow you access to trim off the remains of the channel as shown in pic 4 below. Trim off the remains and clean up the area ready for welding.
I usually cut the door gap section out first, then the front inner wing area and finally the rear section. As everything's braced up there's no risk of the a/b posts shifting. 

Fitting the Channel

First thing to do is to paint the bottom of the channel. Why? Once fitted the bit that sits over the chassis area won't be accessible for painting and you wouldn't want your hard work to rot out again (unless the body is coming off for paint). Also, run an appropriate size tap through the bolt holes on the channel so that all the bolts go in easily. If you haven't got a tap, I've found a stainless steel bolt works well.

Put the new channel in place - I've found it's often easier to swivel the front section in 1st so that the heater tube exit slots in behind the A post. You may need a screwdriver or pry bar to bend down the floorpan edge to slide the channel in place (it's flexible enough). alternatively, get someone to push down on the pan edge from the inside. Put the new body/pan gasket in place and bolt the channel to the floor edges along the sides and the two 17mm's at the front. This means the channel will be in perfect alignment with the floorpan. 
Always trial fit the channel with a few tacks to hold it in place before welding it in fully. Replace the door (to check the gap) and make sure the bolt holes lign up for the running board in relation to the wings. Then  add a couple of tacks at the front A post inner skin (pic 2), B post and the back under the seat will be ok.  Once you're happy, and everything lines up 100%, start welding in in fully - some areas are shown below

If your front bulkhead looks like this pic 1 above you will need to make up a panel and weld that in. Be careful not to damage the master cylinder or any of the pipes present/steering column as it's a bit awkward to do on the drivers side (pic 2 above). If the panel is quite rotten replacement complete bulkheads (pic 3) are available and the repro ones fit ok. Make sure the new bit you let in is correctly shaped and welded in well as this is a prime area for water getting into the footwells.

Rear Door to Wing Panel

Doing a rear quarter panel properly is getting harder as the quality of repair panels available is getting much worse. These are often the wrong length and shape. You also need to weld up the front corner of the panel to create the corner where it meets the door. If your inner wing has gone & the wing bolt hole/bumper hanger area is looking ropey it's much quicker and easier to fit a complete rear quarter from vw heritage as we did to the '72 bug. With the smaller repro panels you get a side of the heater channel on the bottom of them. cut this off the bottom of the panel but leave a bit of the vertical bit as this is welded to the side of the heater channel.
It's very important to get this panel correct as it can let down an otherwise good car.. Once the rot is cut out, trim the panel back to size and  lap the top edge with a lapping tool (pic 1 below) to ensure a nice fit (pic 2 below). Remember - measure twice cut once. If the bottom of the B post is ok, don't cut it away, but trim down the panel so that it joins on the flat edge of the side panel (pic 5 below)

Once it's ready to go in, tack the panel in a few places (ends & middle - pic 3 above) and refit door, rear wing and running board to make sure all the holes and panel gaps lign up and that the panel sits level at the bottom (pic 3). Also, make sure the bottom of the panel is level with the bottom of the door. 
When welding across under the window, go very slowly doing a little at a time and dab the weld straigh-away with a wet rag to keep the heat and distortion to a minimum. Do a tiny bit at one end, then a bit in the middle then a bit at the other end. Eventually they'll all join up with hopefully little distortion.

You will then need to clean the surrounding area back to bare-metal, grind down the welds and apply a small amount of filler to cover the weld. Take your time doing this - don't grind through the panel and when fillering take your time to produce an invisible join. Bare-metal the whole area that will be covered by filler (all the replacement panel and a couple of inches above the panel join). This might sound a lot of filler to start with but most of it will be sanded off. Mix up the filler and apply it in long strokes to get a smooth finish. When sanding it down you'll probably find you need to add a second lot in a few small places if  there are low spots. Take your time with the sanding 240 grit is good for basic shaping, then go over it with 320/400 and apply the primer, 600/800  then topcoat.

Front Inner Wing

Finishing touches - grind the welds down and for an invisible finish, apply a thin skim of filler over the join. again, most of this will be sanded off. Sand the filler down and you should end up with an invisible join. To make sure your repair lasts, spray on a layer of etch-primer, some primer then topcoat. The spray on stonechip is a very good idea for the inner wings and insides of the wings. If you want to use this apply it before the topcoat.

A Post

to be continued as soon as I have the time...