you snip the antenna remote behind the deck. There should be a lable somewhere on the stock deck, that tells you which one the antenna is, Unless you dont want it in use at all, you unplug the whole antenna. Its a big black wire with a plug that goes into the deck.
If you're looking to disconnect the motor because the mast is broken, I think the easiest way is to do so in the trunk, where there is a single plug to unplug.
That's what I did, because my mast is broken, and I was tired of hearing the motor making useless noises when I turn the radio on or off.