I have an alpine deck zip tied to the wires under the seat. Ran an ipod cord off of it and I have it come up just barely between the split in the bench seat. That way when I park and take my ipod out, I stuff the cord head back into the seat so people can't look in and see it. Also when running wires, there will be a few inches of wire that may get exposed when going from the door sill plate to under the seat. What I did was just wrap the wires in electrical tape for that little run. That way if someone looks in, they can't see the wires at all and it just looks like I have an AM radio.
Used to have my stereo hanging from under the dash but didn't do that again after someone broke out my quarter window, stole the stereo and broke my steering column.