You can continue editing the Campaign from your Saved file and simply save it afterward.
I asked a similar question a while back:

http://larian.com/forums/ubbthreads.php?ubb=showflat&Main=81263&Number=642368#Post642368

As for the encounters, there is a weird thing I've noticed, unless the Encounter level is set to the level of the NPC and then manually lowered, nothing happens, i.e. Encounter default is level 1, all NPC's in the encounter are level 3, when the encounter starts they are level 3 still. But raising the default to 3 and then lowering it to 1, lowers it for all NPC's in the encounter. It also will raise all NPC's if you desire that.

Selecting "Give control to AI" is just part of the learning curve with the system. I assume you and your group know that it was the first time and you're all learning together smile