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CC3D running Cleanflight. Not a flashing question. Need advice please.

Hey everyone. I'm still fairly new to the multirotor hobby and had a question i was hoping I could get some help with. I have a QAV 250 running a cc3d. Im interested in switching to clean flight from open pilot. I have found plenty of resources on how to flash clean flight on to it. Just need to order my FTDI adapter. My question is after flashing to clean flight is there anything else I need to know to get it flying. I have heard some people say they had to switch there motors around and some people say the had to use pwm to ppm converter. I was just looking to try and get some clarification to avoid a lot of frustration. Any help would be very much appreciated and I can provide any info needed. Thanks in advance!