The 40G Breeder is a lot wider than the 55g. It gave me more volume for my fuge after i built my skimmer compartment. With all the maintenance and changes you'll make to your sump over time, i figured i'd be better off with the 40g as it has no middle brace to get in the way of things. Since it's wider, I can also get into each compartment a lot more easily then i could with the skinnier 55g.
As for the pipes, are we talking about the sump return line back to the DT? Or the DT supply/overflow lines coming into the sump?
If you have an HOB
overflow, the line should run directly to your sump after the overflow.