The subdirectory containing your WordPress installation is currently and will continue to be the subdirectory of the top-level directory - it won't become a subdirectory of nothing. Domain names are merely strings that point the way to where the relevant files/folders are; they aren't actual physical locations per se.
However, I think I'm now somewhat clearer about what you want to do. As I understand it, your setup is this:
exampleone.com is currently your primary domain. You have
exampletwo.com as an add-on domain, which points to a subdirectory containing a WordPress installation. You now wish to make
exampletwo.com the primary domain.
If that's the case, then you can do one of two things:
(1) Follow the instructions at the tutorial that I linked to above, and then you would change the primary domain in your hosting control panel to
(2) Alternatively, you could actually just physically move all the files and folders into the top-level directory and then change the primary domain in your hosting control panel to
exampletwo.com. Since the database and URL of your WordPress installation will remain the same, there shouldn't be a need to do anything else.
Which path you take depends on your needs and preferences. For instance, if exampletwo.com is the only domain for this hosting account (i.e. you have no other add-on domains), then you may prefer (2). If on the other hand you have multiple domains pointing to this hosting account, then you may prefer to keep your top-level directory clear by using (1).