The mods you have installed replace two completely different things. EUP replaces some of the clothes for multiplayer (GTA Online) character models giving you the choice for a lot of uniforms. The mod you used to replace sheriff deputies replaces completely different pedestrian models. This is why those uniforms do not add up, they are two different files.
If you really want to play with the uniforms those sheriff deputies have you can enter character creation, go into preset characters menu and pick an LSSD deputy from there.
P.S. It doesn't really matter if you install mods to normal folder or mods folder, it should work just as well in both cases