When you wire up GFIs, you don't have to put it in _series_ with the circuit. Freed is right that if it is placed in series it will protect all outlets that are down stream. If you wire individual GFI outlets in parallel, then each one only protects the stuff that is directly plugged into it. Mine are wired that way so that pumps and lights are on different GFIs (same circuit).
One other thing to consider: Since you are having the electrician do the wiring for you, make sure you have enough circuits (to the breaker box) run to handle the load you either currently have or plan to have. Each standard circuit handles 15 amps (really 80% of that is what you should go for -- or 12 amps), so if you are going to have more than that, then have him wire up additional circuits.
Jack