Both ways are working, just don't forget your Cconfiguration-Files (Datalists, Barlists, Integ-Config, Scheduler, etc).
Personally I would take the Second Version for the simple reason that you will have a clean Database and there will be no trouble with changed locations.
If you consider upgrading to DP8 or 9 anytime soon I recommend having the IDB-Files in a Path without Spaces. The w2k8 Default C:\ProgramData\OmniBack\ would be ok, with C:\Program Files\OmniBack you will potentially run into trouble.