You write about pretty libs but put the post into the schematic library category. So you might want to read up on their differences: What is the difference between footprints and symbols?
Lets assume you are running kicad version 4 and talk about footprint libs. (As you mostly talk about pretty directories above)
I tested it in kicad version 4.0.6 and it seems the project local fp-lib-table has a higher priority than the global one. (If a lib with the same name is in both global and project lib table, kicad only looks in the lib referenced in the local table.)
Note that the Nickname (of the lib) is what determines under what name kicad finds the library. This nickname by default is the same as the name of the .pretty directory. But it can be changed using the library manager found under the preferences menu of pcb_new.
For symbol libs in kicad 4 it is a bit different. More details about that see: Any conflict with names of modules and libraries?
In kicad 5 (as soon as it is released) the symbol libs will be handled the same way as the footprint libs are already in v4.