Been cleaning out the ol' data folder and noticed a bunch of bsa files that are not in any specific folder, just loose in the data folder. Mod manager just kind of sloppily threw stuff in there. Are these supposed to be in the data folder or somewhere else?

they're archive files containing all the data you need to run the game. don't delete them.

rofl. BSA are Bethesda Softworks Archives. That's where all the game files (and possibly some mod files) are stored.

The BSAs are highly compressed archives that contain all the raw game data, where as Skyrim.esm and Update.esm contain almost all of the scripting. BSA compression is how they get a game like this to ~6GB.

They're not that good compressed.
Basically the BSAs are optimized to replace the Windows-folder structure, so that the engine can access the models and textures quickly.

The smaller files aren't compressed at all, e.g. shaders.bsa. BSA: 25 MB / Unpacked: 25 MB / ZIP: 1.6 MB / 7z: 470 KB.

The bigger files are compressed but it's a rather simple algorithm, even age-old ZIP can squeeze the files better.
e.g. textures.bsa: from 2.4 GB unpacked to 1.4 GB (BSA) vs. 1.3 GB (ZIP) vs. 1.0 GB (7z)

BSA uses the ZIP-algorithm, and yes it can be better:

Skyrim - Animations.bsa 42365780 -> 40168160 (1133 duplicates) 94.8%
Skyrim - Interface.bsa 34608945 -> 14150057 (9 duplicates) 40.9%
Skyrim - Meshes.bsa 1520899887 -> 1482423428 (34 duplicates) 97.5%
Skyrim - Misc.bsa 177894975 -> 132840928 (453 duplicates) 74.7%
Skyrim - Shaders.bsa 25686897 -> 1621781 (0 duplicates) 6.3%
Skyrim - Sounds.bsa 953785521 -> 741773824 (42 duplicates) 77.8%
Skyrim - Textures.bsa 1388866502 -> 1344588359 (6178 duplicates) 96.8%
Skyrim - Voices.bsa 1458554685 -> 1293664414 (761 duplicates) 88.7%
Skyrim - Voicesixtra.bsa 13016190 -> 11614402 (7 duplicates) 89.2%