To begin with, we need to know WHY you are replacing the compressor? The procedure will be much different depending upon whether the seal was bad, or if it quit pumping or locked up.
If the compressor quit pumping or locked up, you need to COMPLETELY and THOROUGHLY flush the system. This means breaking every connection and flushing, flushing, flushing, flushing and once you're done with that, then flush the system. It would also be best to add a suction side filter.
Do not take a chance on the oil that is in the compressor, unless you are told exactly what it is, pour it out. If you flush the system because of compressor failure, you can pour the correct amount of Ester (assuming 134 of course) into the system, then thoroughly evacuate the system. Since the weather is turning cool, you may have to use heat lamps on the system to get the temperature high enough to boil off the moisture during evacuation.
DEFINITELY replace the filter drier because you will be opening the system. If you are only replacing the compressor because of a leaking seal, you can plug the lines when you remove them to minimize contamination, but still replace the filter drier. Even in this situation, I would recommend thoroughly flushing the system so that there is no oil left behind. This way you can get the correct amount of Ester oil in the system (assuming you are staying with r134.)
I did not notice what part of the country you are in. If you are in a hot climate like Houston, New Orleans or Florida, you should continue returning to R12 and mineral oil after you've flushed the system. R12 can be had for about $29 per can now. Even at this price, R12 is the cheapest major component in the system.
PS: To determine the correct volume of oil, go to www.aircondition.com and then go "Straight to the Board." Post the question with exact make and model and they will post the volume of oil needed by the end of the day.