POR is somewhat spreadout, and if you think you're going to spend much time at all in the restaurant, food court, lobby, or general store, then you should definitely request lodging near that area. I personally don't mind the walking, but my partner did and made sure to mention it every day.
Out of the four mansions of Magnolia Bend, the closest to the South Depot, the "main" depot, is Oak Manor. You just walk across a bridge and then past the lobby and there you are. Although, if you're not adamant about using the South depot, I would recommend lodging in Magnolia Terrace. It's very close to the East Depot.
As far as which area to request, Magnolia Bend versus Alligator Bayou, that's really up to you. The layout of the rooms are identical, but the theming of each is vastly different.
Before making any decisions regarding your lodging, you should definitely check out andrewilley's website at
http://www.portorleans.org. He's got just loads of information, photos, maps, etc that most likely will aid you in your decisions. I know it was and continues to be incredibly helpful to many of us.
And if the website doesn't meet your needs then just post something here and I'm sure someone will be able to help you out.