Was wondering how it would work if you defrag the separate RAID setups.
If RAID 0 is 2 drives together will it be moving files from one to the other to fix them and with RAID 1 will the master drive defrag as well as the backup mirror?
In RAID1 both drives are defragged simultaneously.
Defragmentation works sector-by-sector. As sectors are written, the RAID0 implementation layer will decide which device they're read from and written to. So, yes; parts of the file may move to the other drive.