One of the better ways to hook up a generator is through a manual transfer switch (MTS). The easiest method is to install one that is the same capacity as your incoming power (typically 200 amp), otherwise you have to select which circuits to switch over to a subpanel that is fed by a lower capacity transfer switch.
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Have an electrician install this in-between the meter and your main load center. Then your generator would wire into this MTS and you'd be ready to go. The MTS will prevent your generator from back-feeding the main power lines, yet allow you to operate anything in your home as long as it does not exceed the current capacity of your generator.