Each time I install a new version I have the Data/Settings folder within that versions own folder. In other words I do not have a "central" data/settings folder that I continue to use each time I upgrade versions. Obviously it would be easier but I didn't know if that would be good practice since we're dealing with a ...dare I say it, beta.
I put all ISI mods and all updates in a single folder on my D: drive that I use each time upgrades come out. No issues so far.