In my new 4.9 game, I am far from the tech level I would need for this, but in my former 4.7 game, my 30.000t BBs and BCs each had space for a company of Marines, a single cargo handling system and a boat bay with a small dropship that could carry that company to a disabled enemy vessel.
The Marines would stay aborad the BB/BC, not loosing any readiness and only board the dropship just prior to launch.
Disassembling alien ships: Just scrap it at your shipyard. WARNING: Only 90% sure this will work
Reembarking troops: Um, I realy don´t know. I just assumed (up until now) that after a successfull boarding, they will do this automaticaly.
Boarding chances: Steve posted a formula somewhere, I´m too lazy to look it up right now
Surrendering: When you conquer/whipe out the last colony of an alien race, their ships will surrender (combat capable ships might continue to fight, i.e. missile ships _with_ missiles, beamers).
Boarding is introduced here:
viewtopic.php?f=1&t=1680#p15830 and here:
viewtopic.php?f=1&t=1680&start=15#p16049