yep, shorter the better generally, however Tabetha is right, in an ideal world earthing to the battery is perfect for less interference, just not really practical.

Running the wires on seperate sides of the car is not totally necessary, running them together is fine if they are good quality, but its good practice to try and keep them apart.
And always make sure the main power lead is as big as you can get it, amps not getting enough power is the biggest killer of them.