Make sure the wire from your alternator to the new battery bank is as large as you can find / afford (minimum 4 gauge.) The alternator is setup to charge the engine battery through a 2-3 foot cable, so it will charge first/fastest, and the extra batteries will never top off, since the alternator cannot sense the other batteries being weak at the end of a long skinny cable.
X2 on previous suggestions for an isolator, to protect your engine battery from being used while the engine is off.
Regarding connecting trailer batteries to the in-truck batteries, well... it's possible, but why? It isn't going to work like you think, as one large battery bank. You could buy a bank selector switch, and use either the in-truck batteries or the trailer batteries.