Syncing your changes with OpenACS updates: this is always going to be a manual thing. I don't see any way around that. Your best options are (1) get your changes accepted into the main source code :) and (2) change in as few places as possible. Also get good at reading diffs. :)
I wouldn't worry about it too much. If you're doing mostly cosmetic changes anyway, and someone else makes other cosmetic changes, what do you care? your site already looks like you wanted. If you're really paranoid about it, don't start customizing your module until mainline development on it is finished. You won't be doing customization on the core so you'll be able to (almost, subject to data model changes & such) drop in whatever core improvements the OpenACS team comes up with.