1) I use Montezuma with a child theme. I know it wasn't really designed to need to be used that way, but historical necessities led me down that path. Certain files don't seem to register as being available in the child theme - e.g. breadcrumbs.php and comment-form.php. Even though my versions exists in the child theme, in the equivalent locations, it uses instead the main Montezuma ones. It's therefore necessary for me to recopy my versions of these files into the main Montezuma directory after upgrade. I suspect I shouldn't really be doing this! Am I doing something wrong (other than the copying!)? Perhaps putting them in the wrong place?
2) Any changes I make to the base CSS files in the child theme also don't register, and obviously those in the main Montezuma theme directory get overwritten on upgrade. I doubt this is really an issue, as the CSS actually used is held internally in the database. I do all of my work offline on a development site, then upload a revised database. I guess it would only become an issue were the RESET ALL option invoked on the live site. I mention it mainly in case I'm wrong and missing something, and should be more worried about reinstalling my versions than I actually am.
3) I've tweaked some of the functions. Because the functions in the main Montezuma functions.php file aren't wrapped in an if(!function_exists) conditional clause, I can't just redefine those functions in a separate functions.php file in the child folder, without getting "function already exists" error messages. At the moment I'm just recopying the old (tweaked) version of the functions file back into the main Montezuma directory. I suspect this is a worse crime than the others, because any new functions introduced in the upgrade won't get defined. It occurs to me, while writing, that a partial workaround is to create a child functions.php file only containing / redefining the functions I've changed, then either delete or wrap in an if...exists clause those functions one at a time in the upgraded Montezuma functions.php file. Is there a better way I'm missing (by 'better', I mean 'less work' to be honest!)?
Like I said at the start the basic upgrade worked well, and as theme upgrades are so rarely needed, this is only a minor issue and I appreciate it's compounded by me not using the theme exactly as intended. Therefore if the answer is 'go away and stop annoying me!' I'll understand.
I'm just too anal to resist once the 'Upgrade available' bubble comes up!
(Site is http://s-t-u-f-f.net but as - hopefully - I've caught all the tweak issues, viewing it probably wouldn't help!)
That may well be a better way to ensure all my online Montezuma files match my offline ones. 
