The filter should be close to the output of the compressor...before the condensor... you are trying to keep the condensor ' clean' in the event of really bad situation....
Since you did not follow usual recommended procedure... as mentioned above.... you may have some problem cleaning up your system well enough that your next good compressor will have a long life... lots of good threads on this forum and on Aircondition.com others... most of the philosophy of cleanliness applies to all AC systems...