Keeping customizations across upgrades

[Harley77]

I've made a number of modifications to our Zimbra install that include changes to templates, logos, and the ZmMsg.Properties file. I can create scripts to backup and replace the the files for upgrading, but I know this isn't ideal since my versions of the files could go out-of-date with each upgrade if new additions were made. Is there an "ideal" setup for making customizations that could survive the upgrade process? I would like to have changes persist across all the themes as well as the ZmMsg.Properties file. Is this feasible or do I just need to do my compare and merges as I've been doing?