OK, I have a couple or few cramps so I have an advantage, but here is approx how I attack the job of a Th*rne box, or several.
I pull the box together (or bash it together on the floor) but tighten a cramp across to hold it firm and approx square. Frame runners on, then set the frame runners at the correct height with a couple of frames, one at each end. Tighten the cramp a bit so nothing slips, make sure the diagonals are the same (ie box is square) and screw the sides together with the box firmly on a level surface. Job effectively about done really. By the time you have sorted out the first little jobs to be done, like drilling pilot holes before assembling, you may have made a couple boxes but you will soon realise where pilot holes need to be drilled.
So we now have the sides and ends screwed together firmly, frames just level or a smidge below the top edges for bottom bee space, and the box square. I now pull the side bar/sidewall joints together, after loosening a couple screws if necessary and glueing up the joints. Cramps on, check for square and job done that end. Do same for the other side rails. Check box sits level on the flat surface and is square and leave for the glue to cure. Nearly all the Thorne boxes go together pretty well square with no difficulty, but I always check and recheck regularly. No jigs, like the workshop hive makers!
Nail later 'on the tosh', if required and punch below the surface. I actually pilot and screw all the joints (even the screws are sligthly 'on the tosh'), so that I can continue to the next box without waiting for the glue to cure.
As I am top bee space I initially set the frames height with about a 1 mm strip below the frame bottom bars or if I have several to do, I find/make a piece of wood at top bee space thickness and get that level with the top edges.
I pilot and screw the frame runners, so they can be easily removed/replaced if needed. I usually fit them before assembly, if just making the odd box.
When all is cured I clamp the side bars to the walls and screw together (or if I have suitable screws with plain shanks, I just screw them and pull them together, or you could pilot for the screws and then pull the rails and wall tight together). I do not glue the side rails to the walls. Most of the screws are put in slightly on the tosh.
So my boxes are a relative mass of screws (over 30 of various sizes) but I know I could carefully dismantle the whole box if I had to, should I ever need to replace any parts. Not repaired any in ten years.
If you nail the side rails they may well need clamping if there is any gap (seconds are not always straight), nailing on the tosh and probably glued, or filled later. Screws usually do the job very effectively, I find.
With seconds, I always select where the parts are going to go prior to assemlbing any of the boxes, so that any knot will always drain away, not into the wood, is hidden up behind a top rail or whatever it takes to cover as many of the 'seconds' imperfections.
If you must glue the end walls to the side walls you have the screws to locate the parts after disassembly to glue the joints.
The only time I use my tape measure is to check the diagonals for squareness and I do use a large power screwdriver or two. I hope there might be a few helpful tips for the assemblers to make building their hives more easily. I know I don't do it by the book (or the instructions) and I always have a bag of unused nails, but there we are, that is approx how I do it.
RAB