C&R FFL app and COE app are completely separate. You just follow the directions for the C&R app and send that in to ATF. Follw the directions for the COE app and send that to CADOJ. You can do it in either order. Historically, we waited for the C&R FFL to be issued before we applied for the COE since ATF could take a long time to approve and CADOJ gets the COE approved in ~2 weeks.
Do you want an AOW or C&R SBS/SBR in CA?
FrontSight Training Course certificates available $25, PM for details on them and other options.
No posts of mine are to be construed as legal advice, which can only be given by a lawyer.