Thank you alex for seconding my comment regarding the free version of VMWare.
In tests I've read, VMWare performs Slightly better in most areas and notably better in a couple. The biggest reason to use VMWare, in my opinion, is that is offers FAR better USB support. Outside of that, Both are going to be aweful for anything processor intensive, but for everyday testing/work on things that are not CPU intensive, either will work just fine. Another VMWare advantage is that it supposedly can open and run Virtual PC Virtual Disks.
When you setup the Virtual Machine in Virtual PC, you should have assigned it a virtual hard disk as a file - so you can let CentOS do whatever it wants to - it should only affect the virtual hard disk file.