Your questions are not AIP specific, but reflect a general lack of understanding in how BZ2 works:
Lets start at the beginning: Go to your BZ2 folder and open bzone.cfg with notepad. 
You will see several AddDirResource AddDirPack, etc, addon, maps13, patch13.pak, data.pak, etc. 
These control where the game looks for things. It looks in them in order from top to bottom. So, when searching for say, ivrecy.odf, it will search in addon first, then in maps13, then in patch13.pak, then in data.pak, and then in data folder. It stops looking once it finds it, so the top layer will always be used.  
You can specify a different CFG to launch with, via the /config BLA.cfg command on the shortcut target line. i.e. Target = "C:\Program Files\Battlezone II\bzone.exe" /config MyMod.cfg /win /nointro /whatever other commands u want.
So, placing things anywhere inside addon will make them used instead of the "stock" things. Note that replacing stock files likely will cause you to get Bad Assets, unless they are: .cfg, .dxtbz2, or .wav/ogg. These won't break assets, but anything else will if it overrides a stock file. 
As for setting the AIP, the DLL's control the AIP file names used. Conventional naming scheme is as follows:
AIPBASENAME_[CHAR HumanTeam] [Char CPU Team] [AIP Number Type]
The following are the aip types used by stock:
0, 1, 3, a, s, l
So, Stock13_ aips have the following files for ISDF(human) vs Scion(cpu): stock13_if0.aip, stock13_if1.aip, stock13_if3.aip, stock13_ifa.aip, stock13_ifs.aip, stock13_ifl.aip. 
Next: Creating new AIP sets: 
There are stock AIP .autoreg files located in the BZ2 folder under maps13/autoreg/ I suggest copying one of the aip ones and renaming it to your aips and editing it in notepad to point to your AIP files. 
There are a few folders inside of those adddirresrouce locations that ARE hard coded folder names it looks for. They are as follows:
/missions/ - DLL files must be here. 
/missions/Instant/ - Any .bzn map files here will be loaded into the Instant Action map list.
/missions/Mulitplayer/ - Any .bzn map files here will be loaded into the Multiplayer map list. 
/autoreg/ - This is where .autoreg files are located. They're a new 1.3 feature for automatically adding things to the following lists: AIPs, Recycler Variants, Animals, and STCTF Goals. This is what you'll use to add your AIPs to the AIP list below Insane. (though ordreing i believe is alphabeticle)
/CDAudioAsOgg/ -  This is where any .ogg files go, which must be named cdaudiotrack2 - cdaudiotrack256. These will be used in place of the in-game music when the audio option for random music is on, and will randomly play them. They must be in order, i.e. no gaps in the numbers, for them to all play. i.e. If you put in cdaudiotrack2-cdaudiotrack20, and then skip 21, and put cdaudiotrack22 - cdaudiotrack200, it will not read/use 22-200. 
Other then that, any file can be anywhere within the directory or pak file that is listed in the bzone.cfg, or whichever mod CFG you choose to use to launch BZ2 with. Go forth and explore 
