Yes, you should overwrite. The newer file is better and it won't hurt the regular game or other mods a bit (in fact, most other mods have the same file).
(Actually, I don't think it's ever been asked before - or it would have been in the FAQ )
Ah, sorry. In that case you shouldn't worry. You probably already had the latest version installed an your unzipper noticed this, your unzipper automatically overwrote the file (or not), or AP is one of the few mods that doesn't have this file (but that seems unlikely). If the mod shows up in ModSwapper and works okay, you can safely forget about it.
If you want to make absolutely sure you have the latest version of the file installed (it only solves a minor bug with the backgrounds of the battlefield - very minor issue that doesn't affect gameplay), check in the folder ctp2_data\english\uidata\uidata\layout if the date of your battlefield.ldl file is 1 Sept 2001 or 1 Nov 2000. If it's Sept 2001 (or any other date in 2001 or 2002), is the latest file. If it's Nov 2000, you can replace it with the file I attached if you want (make sure you backup in case it doesn't work - I don't think changes to other files will be needed but you never know).
Of course, you should only do this if the Apolyton Pack works okay. If there are problems with it (it doesn't show up in ModSwapper, it doesn't work, whatever), perhaps that has something to do with it and you need to figure out what's going on there first.