First it get stored locally with whatever job I am working on (or maybe a non permanent location on the network). Eventually it winds up as an Inventor library part at a network location once it has been cleaned up if needed and all the proper iProperties have been filled in correctly.
How the library is grouped is a whole other matter. You can have folders by part types, vendors, mfrs, and sub folders as needed. I have base folders for "iParts," "Purchased Parts," and "Standard Parts" with a variety of subfolder groupings. No matter how you goup it at some point you will wish you had done some part of it differently.
PS for stp files that need to assemblies, I constrain all the dub solids as needed and rename them and set the BOM type as needed. I also set the positional reps. I have only the main assembly shown and a subfolder with the same name for the parts. For IV11 I think you can keep these in your library and change the Pos Rep without IV thinking the library part is changing and needs to be saved. In IV10 it is a problem, so while the assembly resides in the library, the assembly used in your machine etc. is copied locally to that job folder, but the parts remain in the library.
Pete