Here's an illustration of what I have done:
On the main board, IC6 is the chip responsible for driving the positive (red) motor wire. IC5 handles the negative (black) side. The graphic shows the chips how they appear on the board if you are looking directly at them, with the front of the car facing you. If you look closelty at the board, you will notice that one whole side of each chip is connected directly to the motor wires. This is the Drain pin of the MOSFETs, and as you can see, the drains of both the N Channel and P Channel MOSFETs are tied together within each chip. The diagram to the left of the picture shows the pinout of each MOSFET. It is the same for both the P Channel and N Channel. Both the center pin and the tab are connected to the drain within each MOSFET. Keep this in mind so that you don't inadvertently create shorts! Pin 1 of each chip is grounded, so as long as you tie the sources of both N Channel MOSFETs together, you only need to run one wire from the MOSFET board to the main board. The rest of the wiring is pretty straightforward. Just wire up two pairs of transistors, an N Channel and P Channel in each pair, solder the drains together, and connect the motor leads to them.
I can probably draw a complete schematic, but this should give a pretty good idea of how to do it. Basically, pretend the outlines of the ICs aren't there, and solder the corresponding pins of the MOSFETs to the proper place on the main board.