Best way to go is to get an interlock on the breaker panel. It’s a mechanical lock switch that only allows the generator breaker to be on if the main breaker is off. Then run the wire from the generator breaker to the outside of the house. I wouldn’t put a generator in the garage, to much fumes. Then you pick what breakers will be on in the house, with all breakers potentialy available.
To clarify our situation: The generator is stored in the corner of the garage and we wheel it out, as far a we can, when we need to use it, leaving the garage door open. When I get that longer cord, it's going to be operating outside!