Should I prebook tickets to the scavi at St Peters or is it easy to pick them up there? As well, what about an audience with the Pope. Pre register? This is for later September
The Scavi tours fill up months in advance. I doubt that there's anything still open at this point. If you're one or two persons, you can try just showing up in hopes someone is a no-show, but don't count on it. Those are among the hottest tickets in Rome. Don't know about the papal audience question.
I assume you mean for the General Audience on Wednesday's and not an actual one on one audience. For the Wed General Audience you can request them for free through this link: http://www.santasusanna.org/popeVatican/tickets.html
It's worth sending an email to see if you can get Scavi tickets. You'll find the information on vatican.va. If the Wed audience is outside in the square, you can get a ticket to sit down or wander in and stand on the periphery. I'll be going with a church group and the audience when we'll be there (beginning of Oct) is supposed to be in the square. If the audience is in the papal audience hall, you can only get in with a ticket.