You can add mods, yes! If they're simple enough. You can't add really big mods that do all kinds of things though, definitely no overhaul mods. Texture mods might overwrite and undo already installed ones, but that's the whole point right? Event mods might conflict with other events, location mods might screw with the continuity between places by replacing already replaced places, but there is room for you to add plenty of new mods yourself if you're careful about it, plus you can always start over.
And yes they'll have to be installed through Mod Organizer.
After installing new mods it's a good idea to run all of the patchers; FNIS, ASIS, whatever the others were... (look at the guides & tutorials thread for how to take care of that) otherwise Bad Stuff might happen.
If you're new to Mod Organizer too, just learning about how to most effectively use "MO" will teach you a lot about safely adding to or fixing up Perfectly Modded to suit you. Someone on Youtube made a long series of very nice MO tutorial videos which helped me.