Chi,
Here's some answers:
(1) Geneva to Annecy is less than an hour by car; but there's also pretty frequent bus service, which goes to near the center and also the airport. I would suggest avoiding Geneva, but then again, I really disliked it the one time we stayed there, so I'm not unbiased. I don't know where the old part is; maybe we were even staying in it. If so, I didn't think much of it. But the lake area is nice.
(2) I think GPS is usually available as an option, but I'm not sure, since I've never considered getting it.
(3) The problem with seeing the cities, even if only the center, is the time spent driving into the city and looking for parking. I wouldn't even attempt that in Geneva, and my one experience driving in Strasbourg was horrible (it was a busy weekend, though). Colmar is much more modest in size. One option is spend one night in Strasbourg and one night in Colmar, then the other 3 nights at one place in between and take day trips. Or, you cam spend all 5 nights at a centrally located village and take day trips. We've done that, including taking public transportation into Colmar to spend half a day.
As to the last part, I would skip Geneva and go right to Yvoire. I've spent a night in Yvoire, and it's beautiful (if touristy). Geneva is huge, and you already know how I feel about it. As to Annecy, here is what I just posted to someone who asked about what to see Annecy:
"The "old town" center. The lake (one can't miss that), including a walk part way around it. An outdoor market in the center if there is one the days you're there. If you want the link to my travel blog, which has several entries for Annecy, send me a message; the forum rules don't allow posting such links (I've had mine removed before)."
Good luck, and feel free to ask for any more advice.