I have a few packages locally compiled, for example mutt. I have stripped all unnecessary options from mutt, and added it to IgnorePkg. Now when an upgrade is available, i see the changes and decide whether to upgrade or not. In case of mutt, the last two upgrades had added patches which i didn't need. So i just changed the version in PKGBUILD to correspond to the arch repos.
In your case, I believe it's easiest if you change the name of the package to "mutt-custom" or some-such. Optionally you could also add provides=(mutt) if there are some other packages that depend on mutt.
-- дамјан
