The 'extra' tonnage a jump drive can jump is its capacity minus its own tonnage. Just keep in mind there will be extra crew space and armor put in place, so leave some slack there. Crew and armor are not easy calculations to make.
It is typically easier to first design a jump drive, then design your ship to fit in its capacity.
http://aurora2.pentarch.org/index.php?topic=10999.0 this might help when designing a ship.