You can put the cap on in any position you desire, and the clips will end up at many different positions, but you can still get it to run correctly. Just envision it working correctly, but lifting the distributor out, and moving it one tooth counterclockwise. Sitting it back down in place would leave the rotor underneath the cap pointing at the wire that was counterclockwise from the original wire(it may take 2 teeth to equal one whole position). So what do you do to fix this? You take the wire the rotor was originally pointing at, and move it counterclockwise to the terminal that the rotor is now pointing at. Then shift all the other wires around the cap likewise. It will still run correctly, but you have shifted the physical position of the cap.

It's best to keep it like the factory had it if you can, the wires fit better and the vacuum advance doesn't hit anything when you try to time the engine.