To save yourself wiring trouble you can get one that has the controls right on the unit, that way it is very simple to install and hookup to the pre-wiring. The pre configured setups do not use the duct work, from that aspect they are a standalone unit. You may also want to consider getting a low profile unit if this is on the front of a 5th.
I did this last year and here is what I found out, pre-wired is electric to the point of install, no wiring back to the thermostat or pre-configured path for you to add a second thermostat in the room (hence why controls on the unit are an easier choice).
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2012 Sierra 365SAQ
2006 Police Roadking FLHPi