If you have aftermarket disc brakes that were made to mount to the factory rear end they usually will NOT work on an aftermarket rear end.
If the caliper mounting bracket mounts to the outside face of the housing end then they should work. If they mount to the back side of the housing end (normally the case) then they will not work.
If you can tell us the manufacturer and part number of your brake kit we can find out if it will work or not.