I've done it both ways. I've had good luck doing trans separately. After putting the engine in, benching the trans up isn't extremely difficult. Just make sure you align that clutch well so you don't have to redo it after struggling to put the trans in for a while. Definitely not speaking from experience....
On the other hand, though, taking them out and installing them together works well too. You just need to be able to tilt and move the whole thing a lot so one of those leveling things would probably be nice, though I've never used one.
Basically pick whichever one you feel more comfortable doing. Both work and get the job done. If you're not comfortable holding the trans above your body trying to slide it in, maybe go the other route. Separate has been less stressful for me and I like it better.
edit: either way is much easier with a second person. If you're doing it alone, I'd say drop them in together. You can go slow and take your time, making sure you don't damage anything, whereas benching the trans up from below kinda has a time limit. If you have to keep wrestling some wires then it makes it a lot harder, but if you have a person above holding the hoses and wires out of the way and their guidance it's a lot easier.