Both offer the same service as the lodge was changed to full service this past summer (pre-planning, private check-in, staff on duty 7am-10pm daily, lounge open 7am-10pm daily). IMO, it's the overall feel that makes them a bit different. The main building is spread out, with the staff and balcony on the 3rd floor and the lounge on the 4th floor. The lounge is large with lots of seating and it overlooks the main lobby. Big windows look out over the courtyard. You can't book a certain view, but you can request either the lagoon/beach, garden/pool or marina/castle. It's just not guaranteed. Rooms range from standard size to concierge to deluxe, honeymoon and suites.
The lodge is located in the Sugarloaf building, which is very close to the main building. It has a much more cozy feel to it and I always use the phrase "bed & breakfast" when I describe it. The staff, lounge and seating are all located on the ground floor lobby and it just feels more cozy and personable. There is no TV in the lounge (main building has 2) and it lacks any view. It's a nice, quiet refuge after a few hours in the parks though. Room views are either of the marina (no castle view, but you may see the fireworks) and garden/pool. Room styles are either standard concierge, with 3 lodge tower rooms available by request (not guaranteed) and suites.
I've stayed in both and personally I prefer the main building. It has a certain ambiance, but it can also feel a bit cool because you don't have constant contact with the staff. We've enjoyed our stays in SugarLoaf very much though.