I would suggest working from diagrams rather than from line-by-line notes, at least while in this phase of rehearsal. You can then refine these diagrams, convert them to line-by-line notes, or do whatever else as the choreography becomes more precise and permanent.
It might also be helpful if you do some triage. As a stage manager, you have several priorities, and they run something like this:
1) Make sure nobody dies.
2) Make sure nobody is injured.
3) Make sure nobody is nearly killed or injured.
4) Make sure no property or equipment is damaged or destroyed.
5) Make sure the show keeps moving in an orderly fashion.
6) Make sure the show is artistically interesting and correct.
Essentially, safety and efficiency always trump art.
If the director is giving you dozens of notes and you can't keep up, focus on the Really Really Important Stuff and--at least for the time being--ignore the lesser information. (For example, you mentioned that your show has set pieces moving across the stage and through the wings. As a stage manager, you should be much more concerned with ensuring that these set pieces clear the stage without colliding with any cast members or other pieces of the set than you should be with the artistic content of the show, so focus on getting good information about these set pieces rather than on choreographic details: you will need to know about these set pieces, while you do not necessarily need to know that the third line goes kick-kick-smile-kick rather than kick-smile-kick-smile in the 27th bar of the 4th number.)
