You don't need to keep any gathering materials in your bags. I now keep all mine in my cargo hold.
It seems obvious to me now as you send your crew members away to make stuff. But in WoW I had to have my mats in my bags to make stuff. So I just assumed SWTOR was the same. It was filling up my bag big time until I got sick of it and chucked everything in the locker and tried it out.