|Key image courtesy of Jaldaboath :)|
Once that's done, just save it and close, then rename the modded stage to match the 3-letter prefix you just swapped in. In this case, I change BRA.tex.emz > LBX.tex.emz and BRA.emz > LBX.emz.
Now you just copy those modded stage files into your [install dir]\resource\battle\stage directory and overwrite what's already there. Just make sure you backed up those original files first, in case you change your mind later.
UPDATE: If you would rather not overwrite any of the files, there is a way to supersede the original stages in a non-destructive way. Instead of adding your modded files to the above directory, instead go to [install dir]\patch 1a\battle and create a new directory named 'stage'. Put your modded files in there and the game should use them instead of the originals. (thanks to Nemesys_Syndrome for the tip)
That's it. You're done. Now, go try it out and make sure it works :)