I don't know how much "Honeymooning" you're planning on doing on your honeymoon, wink wink nudge nudge and all that, so take this with a grain of salt.
Yes, the rooms in the Magnolia Bend "mansions" seem prettier, and the Alligator Bayou rooms seem more rustic. But bear in mind, the Magnolia Bend buildings are bigger, which means the potential for more people walking past or around your room, to say nothing of sounds above you if you're on a lower floor. Whereas the Alligator Bayou buildings are smaller, so you have better odds of getting some place a little more secluded, with less "foot traffic" traipsing around.
Personally, I'd shoot for building #24 in the AB section, and request to be as far back as possible. True, you're about as far away from the main building as you can get, but it would be more secluded. I believe that's the building where we stayed on a leg of our honeymoon. Also very close to one of the quiet pools, which came in quite handy considering we went during Spring Break and there was never a spot to be found in the main pool or around it.
Either way, you should at least have it noted on your reservation that you're on your honeymoon and would like as secluded a room as is available.
Also, while you say you've booked a "standard" room, you should see about getting a room with a king-sized bed in it. Something to think about...
