When I've done it;
Both pairs wait in one corner.
First of the pair goes out on the bell, jumps the whole course, then when finished goes back to the corner, the second of the pair goes out and jumps the whole course, then goes back into the corner.
Overall time, faults, refusals counted.
For SJ yes, as the others say. For XC, you go round as a pair and try and jump every fence together and as well as penalties for refusals and stuff, you get marked on how together you are, usually out of 5. The lowest score wins.