SK, I had some of the same questions when I got my PC. I had E-mailed Terry at CMA (where I ordered my pads) to ask him about "high points" on the surface of my hood and fenders, and moving between panels. He said not to worry about ridges in the hood, as the PC just cannot abrade away paint fast enough to be a danger in those areas. My experience confirms this and I have nothing but good results with my PC.
As for moving between panels (hood & quarter, etc.) Just work each panel individually...if I need to move from the hood to the fender, I finish working the hood, turn off the PC, move and then turn it back on. If you need to work on the edge of the hood and are worried about damage to the fender (or any other panels), then I would use some 3M tape and cover the edges. A few minutes of careful taping before your detailing session will come back to you tenfold in the ability to work quickly and confidently. Also tape off your trim (helps to stop staining them) Really, the only time I move from one section to another in rapid succession is when I am laying on a coat of Blackfire...all of the other steps are done to one panel at a time.
On to your question about pads...I have both 6" and 7.5" pads and use them with my 6" backing plate. I also have the 6" counter-weight installed on my PC. They both run very smoothly and I have had no problems. There is a place in my heart (awww) for each of them. I really like compounding and polishing with the 6" pad and finishing with the 7.5" for liquid wax, sealants, etc. I prefer the 6" for the heavy duty work because I can work a smaller area at a time, and I think I get a better "feel" with the smaller pad. Your mileage may vary....good luck.