Saves shouldn't be a problem at all as long as you remember to always load the appropriate campaign. I currently have two campaigns... the one I started at launch with Veronica's Vanilla Vikings, and one that I'm testing personal mods on for my next full campaign. I keep two copies of the VersionManifest.csv file and copy one back over when appropriate... either OriginalVersionManifest.csv or ModdedVersionManifest.csv. To make it work, I also make sure that I never mod files in place... they get copied to my mods directory and the modded manifest points to the copy.
In any case, I always wanted a mod manager with an option to select different mod sets and rename saves so that you can't accidentally load an incompatible one. Wish I had time to spend on it.