Generally the V4 or M4 model is loaded first, then the additionals like Aiko or Hiro or Freak injection files.  Then I usually go for the base morphs, the ++ morphs, Enhanced, Elite, ect.

As long as you have the base V4 or M4 started the other sequences don't matter.  I hadn't gone through the DS manual since I learned on my own, but I would suggest maybe finding the pdf file in your Studio folder and seeing if that may answer a few questions?