I personally would not recommend editing straight from AMA, but a lot of people do and they seem to get by just fine.
Keep your media organized. Once AMA volumes are opened, do not move or rename any files or folders from with the media came from.
Edit your sequence.
Consolidate & Transcode your sequence into whichever Drive you want and Convert to the format of your likings.
This will make MXF files of ONLY the master clips used in the edit.
If you need all of the media, then go to your AMA media bin(s) and Consolidate & Transcode the clips in a batch.