What they said above, however to have a complete answer to your question, BAT also uses JSGME (JSGME.exe in same folder as il2.exe or IL-2/BAT installed folder). JSGME is the JoneSoft Generic Mod Enabler, which is a freeware tool that helps gamers add mod libraries to their games. In BAT there are some features that can be enabled if you so desire, and JSGME allows easy enabling/disabling of certain features. JSGME is a good way to fastly add a mod or feature to any program, but at the expense of drive space, because of duplication and keeping up with what gets overwritten and backed up.
To make a long story short (... too late), BATMODS is the folder where BAT's JSGME keeps its MODs... (JSGME allows the used to define where the mods are... it just happens to be BATMODS for BAT.) You can look at that directory, or you can start JSGME to see what features you can enable.
This is different from the #WAW3, etc folders. Those are for you to install custom mods, like additional planes or features released between major BAT upgrades/versions, although make sure you read on how you have to make changes to certain text files to enable certain mods, like planes (you need to add entries to some files, or they won't work), namely "air.ini" at #[WAW or DOF or SAS or TGA or JTW]3\STD\com\maddox\il2\objects and optionally (if you want nice text) "plane.properties" and "weapon.properties" at #[WAW or DOF or SAS or TGA or JTW]3\i18n.