How to modify/test Upgrade/Incremental/sql..sql script?
If you're targeting the 4.6 branch, then put the upgrade script in the latest 4.6.X.mysql.tpl. If you're targeting the master branch, then use 4.7.alpha1.mysql.tpl.

As a rule of thumb, we try to minimize schema changes in stable release branches (e.g. 4.6.x) and instead put them in master. But that's not absolute.

The difference between a bugfix and a new feature is a bit academic. When a user installs vX.Y.Z., the upgrader needs to apply all schema changes needed to match vX.Y.Z.