Hey Troy,
I have been running both versions at the same time on 2 or 3 diferent computers and have had no problems. If your going to run version 6.0 do run at least sp3 with it. And keep track of what version you are opening a program in. I don't think it would be a good idea to recompile an exe in ver6 if you intend to keep it in version 5(for instance you have no intensions of upgrading current users of that program or you are working with another programmer that only has version 5)