I'm pretty sure the javascript has no idea which file it has loaded from, so there shouldn't be a problem merging it, however...
Personally, I'd keep them separate. It will make it simpler to co-ordinate versioning etc. For most repeat visits, the script will be cached by the browser anyway, so 2 vs 1 isn't really a huge issue. But when you do upgrade one (or the other), the client only needs to download half as much. But again, since it is generally cached it isn't a biggie!
So for simplicity - keep the scripts in their original forms. Given your opening comment "I don't know too much about javascript", this is by far the best approach; I don't mean that disparagingly - simply that if something goes wrong, you don't want to have to find if you broke it, or it was broke already.
Edit: it also makes it easy to re-order, for example if you are using two scripts that use the same terminology like $
in jQuery, which also supports a mode with the explicit naming.