"What is the difference between having matching side covers and different colored ones? Also do they bolt right in just like the stock side covers? Can I use ,y current running tail light and fender?"
This was my experience with Burton Bike Bits parts and my 1973 Commando - it may be different with parts from other suppliers/different year Commandos:
When you purchase all the Fastback parts, the fiberglass parts - tank, side covers, tailpiece - will be the same color - from Burton's, as I recall, the choice was British Racing Green, yellow, and (I think) red. So if you want a different color, the parts will have to be painted. That's no big deal but I wanted BRG so I didn't do any painting.
The current fender will not work - actually, it will "work" just fine but it will look odd because the FB fender, which is black, not chrome, is much shorter in the rear than the standard fender. It barely extends below the tailpiece. The fastback license plate holder functions sort of like the "rest" of the fender.
The side covers required considerable work with a grinder and drill to get them to fit properly, though none of the grinding was on visible parts of the side covers. I had to fabricate the metal bracket for the left side cover that locks it in place. There is no bracket supplied. You might be able to remove the bracket from the roadster side cover and position it where it will work on the FB side cover but the covers are quite different in dimension plus I didn't want to do anything to the oem cover. The right side cover needed spacers attached to the underside of where the cover mounts to the oil tank to raise the cover to the proper position. If you mount it to the tank without the spacers, it is too low on the bike. The spacers were just washers JB-welded together/to the cover.
The FB taillight fastens to the tailpiece, NOT to the fender/over the frame loop. If your 72 has the smaller, older style light - you just use the light/lens portion of your existing taillight, not the housing itself, and it will attach to the tailpiece as oem. If you have the newer, large square taillight, it won't work at all.
The tailpiece also required a lot of grinding for proper fit/clearance - again, not on any visible areas. The rear fender holes did not line up well enough with the mounting points on the bike or the tailpiece so I had to drill some new fender holes and enlarge others. Again - nothing visible was affected.
The FB seat tabs were too short to properly be engaged by the knurled seat nuts so I had to weld approx 3/4 inch of additional "tab" on the seat. The tank didn't need any work on it per se but the rubber padding that supports the roadster tank on the center frame member is totally wrong. I had to build up probably 2" of padding to properly support the tank. The tank padding is very much a cut-and-try operation but it's critical to have just enough to ensure no chance of vibrating parts grinding a hole in the tank!
Only other thing that I can remember changing was adding the full-coverage fork gaiters.
My goal in doing everything was to be able to quickly convert the bike from FB back to Roadster relatively quickly. Therefore, NOTHING on the basic bike was changed other than the rubber pad that supports the rear section of the tank. But that is quickly removable and the oem padding/tank can go right back on. In truth, I will never return it to roadster configuration so I probably worried more about that than I needed to.
I expected to convert the bike from Roadster to FB in a couple of hours...took me two weeks! I ASSUME that back in the day, the FB parts supplied to the factory actually did fit without all that modification, otherwise every fastback was very much a "handmade" vehicle which would have played havoc with the bottom line.
As noted in an earlier post, you will need: tank, side covers, seat, tailpiece, rear fender, license plate holder, fork gaiters, maybe the older style taillight. (I think that's all but I could be forgetting something...)

I have probably missed a few minor points but that should give you an idea. It was definitely NOT anything close to "bolt-on."
This added a bit later - If you are positive you will never return the bike to its current configuration, you could probably use the current rear fender, cutting off the portion that would extend below the tailpiece and drilling the appropriate holes for the tailpiece. I don't think the chrome on the rest of the fender would show at all if you did that...though I could be wrong.
Oops - this added much later: You will need the FB-type reflectors for the sides of the tailpiece and the front of the bike (forward of the coils). The FB reflectors are different than the standard reflectors. Some people don't use reflectors but I like them. You will have to drill the holes for them in the tailpiece.
Good Luck.