well, your best bet would be to run the wires underneath your door sills (the plastic or metal running along the bottom of your car just next to the carpet). there is usually enough space to hide them in there completely without worrying about stepping on, or cutting them.
however, if you must run under the carpet, the "bubbly" effect is really gonna depend on how much it raises from the wires. try to keep the wires as close to your door sills as you can, so no one steps on or crimps them. if you notice any undesirable bubbling up in the carpet, use a light coating of spray adhesive around the wires, and just press them or weigh them down as it dries.
Also.. if you do run them under the carpet try running power cables along the "transmission hump". Usually the carpet raises slightly as it at the bend. Since power is the largest cable generally... it will help.