well best buy would just charge custom labor which is about 70 dollars per hour, however most of the time if they have a good car audio senior (like me, haha) we will discount that down around half that to gain return customers. I would get the door triggers put on right and have them reprogram it for you, as the alarm really doesn't get turned on just powered up and programmed.
Alarm/remote starts aren't super hard to install, but they are really in depth installs, it shouldn't take more than 2 hours for a decent installer to troubleshoot anything as the install itself is only 4 hours or less.