Some people have moved the pickups on the tanks to the bottom for electric pumps, but honestly I wouldnt recommend it.  The reason is that with any small fuel leak (hose/fitting/etc) and you will end up with a bilge full of fuel.  Thats the reason for the top pickups on the tanks, think its a Coast Guard regulation, but not sure. 

 Where is your fuel pump mounted now ?  And what pumps have you been using ? 

 My last 2 boats have had electric pumps with top pickups on side tanks.  The only issue I have had was on my last one when the fuel got low and the pump would get a gulp of air.  That thing had alot of trouble re priming its self when that would happen.  Sometimes I would actually have to blow into a tank to force some fuel to the pump, then it would work fine again (POS copy of a Holley pump mounted on the transom).  The boat before that used a Carter pump mounted on the back of the motor and that thing never let me down in 8yrs of use.