I am about to jump into some chroma keying using final cut pro X
But I was just told that I should use Motion 5 instead. Should I input my master file into motion 5 ?
Many of the clips in my project need keying.
Who told you you should Motion 5? The keyer in FCPX is exactly the same as the one in Motion 5 and it's by far the best chroma keyer you can find in any NLE. So unless there is any other reason why you need to do this work in Motion 5: just stay within FCPX.
If you need to go to Motion for other reasons then yes you can export your FCPX clip(s) as a master file and import these master file sin Motion. Or in Motion you can access the Original Media folder of your FCPX Event from within the Media Browser and work with these instead.
When your work is finished you either export the keyed out foreground as ProRes 4444 with an alpha channel to key it over your background video in FCPX, or you put the keyed out foreground over its background in Motion and you export as ProRes 422.