I can emphathize, though, on the hardware side, it is relatively simple to understand what creates the logic for the SOPC Builder system. i.e.: It is really only necessary to revision control the PTF, QSF, and the QPF files, and, perhaps, any custom components. All of the rest would be overwritten by SOPC Builder the first time you generate/re-generate anyway.
With respect to archiving whole projects....that should be a separate undertaking, and only done at specific milestones throughout the course of your project. A "golden source" should always be kept pristine, or as close to it as is possible.
On the software side, it's a bit messier. The best approach, that I can think of, is to follow the "software template" examples (as much as possible) with your own code.
As far as what RCS to use, my only preference is non-VSS. MS doesn't even use VSS on their own projects :-)
Cheers,
- slacker
EDIT: You could also take a look at what Altera has to say (
http://www/literature/hb/qts/qts_qii54017.pdf)...