newbie- edited templates, mods and upgrades

[doob]

1) If templates like FORUMHOME and navbar have been edited in a template do they revert when performing an upgrade? Or are template edits stored in a style, thus in the database? Basically, if half of the navbar code has been deleted, recoded and then an upgrade from say 3.8.1 to 3.8.6 is performed...will all the custom coding be reverted or broken?

2) Is there a preference in the VB programming community to perform template modifcations via a mod script, or just dive into the individual templates and start hacking? For changing basics like navigation, rearringing the default page layout for things like albums and posts, etc., if we aren't looking to distribute a package to the community, just work on our particular site, is there a preferred way of making changes?

Any input really appreciated!
doob