There are some pictures of the auxiliary in my '46 in my signature, along with a video of how it drives.
Mine is mounted with the rear output in the approximate location of where the carrier bearing once would have been. It is important that the shafts of both transmissions and the pinion shaft of the differential be aligned, and the angle of the driveshafts (resulting from the difference in height between each component) be within the allowable specs, that I believe Grigg linked to. I used a carpenter's square placed over the flats of the yokes with the shafts removed, a plumb bob, and some careful side to side measurements all measured from the main transmission as the reference to get the aux box lined back up after some maintenance a few years back.
My shifter for the aux box is mounted to a bracket made of some angle iron bolted to the side of the main transmission in the same manner that the manual (non-vacuum) 2 speed rear end shift lever would have been. (the 2 speed rear shifter is nicely illustrated in my Owner's manual but I've never seen one in person, only the vacuum type). Shifter comes up through the floor to the drivers side of the transmission in the mid to rear portion of the removable floorboard. No idea if this applies to your model truck, but it is an illustration of an install.
