I'm not a spa person so I wouldn't do it at all, and if I did a spa I'd probably do the spa at Chaa Creek rather than Maruba.
But as to the beginning or end of the trip, I think it's primarily how you want your vacation to go and how you respond to things. I suspect some people could relax better at the beach and some at a spa. Ambergris Caye is very laid back, but because the beaches per se are generally not a big draw it's not like going, to, say, Anguilla, where the beaches are everything, just lying out on the beach (other of course than good food). On Ambergris, many visitors tend to be fairly active -- going on snorkeling or diving trips, walking around town, go out to different restaurants and bars, taking mainland tours, etc. So while it's relaxing in a way for a lot of people it's a fairly active relaxation, not just vegging on the beach.