i sort of know what you mean.
you will need to have the return to the main tank near the top. i dont think there will be a problem with having the engine return near the bottom. there wont be enough pressure in the tank to force fuel towards the engine via the return.
the only down side is that there will "hot" fuel near the feed to the main tank.
i would get a new tank with the correct positioned lines, but if you cant then i guess you will have to use the setup as stated......