Scott,
I'm in the process of doing my only two trapouts, so I'm green at this also...iddee is pretty much the trapout "go to" man on the forum, so I'm sure he'll weigh in.
My 2ยข....
1) Bottom board with the one way exit will probably work, but will make it tough to monitor if you still have bees emerging compared to a wire mesh cone.
2) If I understand what you're asking, I don't think vertical or horizontal would matter.
3) You can use a "queen right" hive, or simply give them a brood frame with 1-3 day out eggs, and they'll make there own queen.
Good luck!