It can be a burden BUT what I found out for every upgrade that I've done I feel somewhat energized. I look forward to each new version and take the opportunity to try something different from my last design. It's all about the creative process.
If you are able to, do your upgrade on a testing board. Apply all of your function and template hacks. When you are satisfied with your results, upload the upgrade (default UBB) files to your open board, then right after upload your hacked files. Your upgrade with the hacked files in one try. This way your users won't be disrupted by the process.
