1) Do whatever you want with your logbook. I just write my student name and the lesson we did.

2) Are you flying the simulator? Log as Dual only.

3) Log simulator and dual only in a student logbook.

There are places in the back of the book you can put endorsements and in the very back there is empty sheets, where I put additional endorsements or I will put ground work. Can you provide a little more info for the last question.