I put torque boxes in my 66 last year. I'll give you my $.02. I used 1 piece Spectra. I cut them apart. I did a fair amount of fitting. The 1 piece box actually contains the inner portion of the floor board. Putting the whole TB box in you're doubling up that portion of the toe board that normally would be doubled up at the factory. If I had to do it over I would only install the outer portion of the TB. This more accurately represents what the factory would do. I would buy the two piece version to save time cutting the box apart.
I decided to install the inner portion of the box. My thought was it may stiffen it up a little more and can't hurt. I don't know if this is a valid assessment. I used weld through primer. I wouldn't use it next time. I felt it contaminated the welding and made it more difficult to get good welds. Afterwards I used 3M cavity wax with a wand kit to spray inside and rust proof. Before that I took a can of spray paint with a nozzle of another can with the red tube to spray some paint inside the box.
I'm not saying you should or have to do what I did, just my comments on doing it if helpful. I have pictures someplace. I did a post on my install, maybe you can find it on a search.
I used the 1 piece Spectra boxes as well and drilled the spot welds out to separate them, much easier to install this way unless your toe board is being replaced as well. Btw, I bought Dynacorn branded ones, thinking they'd fit better. I was wrong, the Spectra ones required less work for me. My drivers side went much smoother than passenger side. Drivers side just required grinding off edges to fit, the pass. side I had to cut the flange off where the outer welds to the rocker because it was too wide. Also, I'm in full agreement with Tom as far as weld thru primer goes. Perhaps what industry uses is good but the stuff in spray can for consumer use is crap in my opinion.
I used the 1 piece Spectra box drilled apart and installed per piece with quite abit of fitment needed, in retrospect it would have been a better idea to have installed them prior to doing the floor pans
There are two versions of the Spectra Crappium torque boxes. There is the older style that allot of mustang parts places are still selling because it's stock on the shelves. They are garbage. They are very rough approximations of what they should be. They are way way out of shape as assembled and even after you take them apart and get the angles bent right you will find some pieces are just too short like the floorpan side doesn't reach high enough. They don't reach to the fender aprons etc.
Now then there are the newer versions which are much more like the pictures above which are 100x better and can be fit without having to add metal to the boxes.
I have also stopped incorrectly using weld through primer. It is meant for the back sides of metal you are welding where you won't have access to prep and paint. It is not meant to be welded through on the face side. Prime and paint your parts drill your plug weld holes and then use a hand held little sand blaster gun to clean the weld area of paint. Way way better overall and you have perfectly clean steel which makes welds much easier especially since some plug welds can be quite deep.