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i don't have any experiences with custom template yet myself. so far, what i have done is changing the template php files themselves in my test environment and got it uploaded to my production machine and got the module updated.
others please correct me if i'm wrong.
for every changes we made in the application (php file), make sure to update the module (might not neccessary if what we change is the includes file? but hey, just update the module).
for the template, clear the template buffer files, and regenerate the template. it should pick the latest template.