Well you will probably get better answers but since nobody's responded yet I'll take a crack at this.
#1 I generally put procedures in the PLAN section and make templates for the ones I do commonly. I don't see a problem putting them in the assessment section though, although I generally reserve that for diagnoses and elaboration on what I think is going on.
#2 I also still use the paper superbills and give them to our billing service. Since the great majority of codes I use are common E@M codes I usually go ahead and enter those anyway on the billing screen since it is nice for my staff to be able to refer back in AC and see what I coded. For things I don't do that commonly I just go ahead and hit save (on the pop-up billing screen) - a window comes up asking if I want to enter a CPT code and I answer NO - the note then saves, and I manually enter the CPT on the superbill. For stuff I don't do commonly I have to go back to my coding guide and look them up. You can find them in AC but the book is easier for me to find codes.
#3 Can't help you there, don't need or use that feature very often. Seems like you could have the nurse put it in there when the patient is checked in if there's not a more elegant way to do it.