Jack,

Behind the seat is preferable in my opinion as in your case you can have fuel at your sump, but still have water or trash stuck at the bottom of the header tank that doesn't make it down until you're running and everything is churned up. The lower mounted tank also has the supply line running out the side with a little bit of unusable fuel so if anything is in the tank still it has a better chance of staying at the bottom of the tank and running out the sump.