manual registration mark settings?

we have the fc-7000 & from reading past posts here & looking at the graphtec user manual I am still confused. We are going to print & cut sol gold engine turn gold. I am using the valujet64,graphtec fc 7000 & flexi 8.
from reading signgolds spec sheet it is recommende to use a manual registration reading & not the arms. my question is do I layout registration marks in my design & then read the off the graphtec or can I use the type 2 that I would typically use & read them manually. If it is just an issue of the material having to much reflection could I just cover up the registration marks, draw them in & use the arms setup. I hope this makes sense this job is quite large so I do not want any screw-ups. Thank You ----Sean