The difference is simple, the
tpls suffix at the end of the filename indicates that the file has all the Bootstrap templates inside, and the others don't.
If you try to use the
ui-bootstrap.js file you will receive an error because the compiled code doesn't find the templates, and you must provide templates for all the widgets.
Perhaps this is not a good idea when you want to override one or two components, so consider using a custom build. The following technique will be very helpful.
You can create your own custom build for UI bootstrap and pick only the components you need at http://angular-ui.github.io/bootstrap/#/getting_started.