I run Inventor 9, but its generally the same, right?
As for your question, yes, after you move constrained things and save, it loads that way the next time. However, once you try to grab anything and move it, everything snaps back into place. If your constraints were not perfect (a term hard to explain) the parts sometimes dont go back exactly how they were. Ex: constrain two faces 2 in apart, it might go back to 2 in away on the WRONG side. Its anoying sometimes.