Russ,
Tick the ‘create archive’ option in Pac Control, That will ensure that a date / time stamped zip file is made for you every single time you download.
Done.
This is usually enough. To top it off what I do is in the power up chart I throw in a date time comment that has a summery of what I changed/added.
You could also use a software versioning system (SVN for example) to manage the zip archives. I never did, I just backed them up nightly and relied on the comments in the power up chart.
Ben.