Remote fuges are easier to deal with for several reasons. First, having a good bit of volume on top of your pump is a nice fail safe for running dry. Second, a remote fuge is easier to take off line. There are more like size issues regardless, if I were to go in sump with a fuge, I would put it opposite the skimmer section with the pump section in the middle. With the fuge plumbed seperately taking it off line is done by a turn off a valve.
following - i just have stuff thrown in my 10g sump for my 55g dt and would like to learn how to make baffles or if it's really needed. The water passes from one side to the other anyway so I don't have any bubbles or anything so I don't really feel baffles are necessary. I have chaeto and culerpa in a net breeder box that I stir up once in a while but no lr or sand.
My skimmer section I raise off the bottom and set my weir at the ideal height for my skimmer. Top clearance is the limiting factor for how high off to put the skimmer section floor; this gives me added volume in case my top off fails. I use a single pane, but an under over wier should be more than enough. Bubbles shouldn't be a problem on the fuge side; I would use a single pane wier set about an inch below the top of the tank and let it spill over, or set it all the way to the rim and drill for a bulkhead and 90 els.
A ran a small single chamber fuge/pump/skimmer all in one for a few years in my old forty; I returned the water through two tlf rx's hanging on the side of the dt just to save on pumps and space. It sure is easier now having a dedicated 40b mechanical sump. My rx's hang in the tank so any small leaks are contained. The difficulty is keeping myself from tossing in extra lr or wanting to turn it into a frag tank, so vacumming it remains quick and easy.