I've done this once - I treated my rep pieces as two separate productions, and I kept two completely different books. We did use the same set (at least most of the pieces) and our light plot was the same. Since you're sharing the set and light plot, that should help you immensely. What should be kept in your mind are the props and costumes - which I assume will be different. At least, they were in my experience.
Due to space limitations, we couldn't have both shows worth of props sitting out at the same time (and for those overlapping actors, it would only confuse them to see last night's props), so we made a plan. We labeled the 1st show directly onto the prop tables/cabinets. When it was time for the 2nd show, we would store all of show 1's props into boxes labeled for each area and put them away in the trap room. Then we put down a rubber shelf liner that had the show 2 prop table layout taped on it, onto the tables and in the cabinets, then put out show 2's props. (You could also do this with butcher paper.) Then we'd put all of the shelf liners and show 2 props away when it was time to go back to Show 1. Worked out well for us.
As far as the costumes, due to the size of the casts and the space available, show 1 couldn't exactly be put away, but we made best efforts to set those items out of the way, so that show 2 had room. Depending on how dressing rooms are laid out, actors need to be warned that the space is shared (only those overlapping would not have to worry about this), so show 1 may need to store their makeup/personal items out of the way, so that the actors for show 2 have room to get ready. And vise-versa.
I hope this is somewhat helpful. Best of luck to you!
