I think airlineapps is the only one that has you seperate PIC from your instructor time. I filled mine out like I'd fill out a logbook so for example if PIC was 4000 and instructor time was 1500, I'd put those number in the respective columns without doing extra math.
As far as the boxes go, I checked every single one I have or had/did. If the computer is hunting and pecking it probably is scored in a way the higher level is what you get credit for.
I worked for XJT and they're still XJT so I got lucky there. However, after the merger their address changed from Houston to Atlanta. I use the Atlanta address on apps even though I didn't work there when it was ATL because I assume the point is so they can track down the company.
Anyway, I haven't gotten a call or anything, just a fellow applicant so thought I'd share how I handled it. Hope that helps! I'd like some detail too. I always wonder what documents to upload besides a resume. All the applications are a mystery in themselves. Like if you have a box you write an aircraft type...will B767, B-767, Boeing 767 all trigger something or only one of them? Etc...