Boxer does not currently support making .app files, nor can you simply rename a .boxer file to make it into a .app. OS X .app packages are more elaborate than you might think, and to the best of my knowledge there are no automated tools that will turn a DOS game into one for you - the DOS games I've seen that have been turned into Mac apps were created by hand.
For assistance with the process, it would be best to contact whoever made the .app directly. That said, it should be possible to duplicate the existing .app, right-click on it and choose "Show package contents", then copy your DOS game files into the package in place of the game files that are already inside it (which are probably located somewhere in the Contents/Resources folder). You may then need to edit the DOSBox configuration file within the app to ensure it has the correct settings for the game, and if the person who made the .app has tinkered with the application's name and other metadata then you'll need to edit the Info.plist file to update this too.
(On the other hand, Boxer's game packages have most of the benefits of a .app without the fuss involved in creating one, so you may find it's not worth the effort to go through that process by hand. Future versions of Boxer may offer the option to create standalone .apps.)