About the alliance/non-alliance question, I think attacking an ally has a negative affect on your influence (you can't be trusted). If you attack a faction and you both have mutual allies, those allies will make a decision as to which faction (your or the one you're attacking) they will break their alliance with.

If I understand your second question, the only affect I'm aware of is that loyalty goes up due to the presence of the armies (Smile for the nice soldiers, Roger, and get the king's banner out of the trash can and hang it out front of the house...)