While you are doing the body work, don't worry about the gaps until last. I usually let the filler bridge over the gaps. This makes blocking from panel to panel much easier, especially if it's through a curve. (think a 69 Camaro going from the door to quarter panel)
I then just use a cut off wheel (slowly) to cut the filler open that has bridged over the gap. Then use a 3" roloc to grind the rest of the filler back to the metal. Always be careful.