Sorry i havent had more time to add details on my suggestion lately.
You run it between whatever your positive line is and the computer. The idea of the DC to DC converter is that regardless of the voltage level and fluctuations on the input side the output ends up being a rock steady output at whatever voltage you select.
Let's say you want a clean uninterrupted supply to the computer of 13 volts at one amp. If you find a converter that takes a 9 to 14 volt range with a 1 amp output then it doesn't care what the generator output is or battery voltage is or what the rest of ciruit draw does to the voltage it always outputs 13 volts solid. It will keep the 13 volts until the voltage into the converter falls outside the input range, in this example 9 to 14 volts.
I just picked some randonumbers here so you will have to choose what your input range is, max current draw of the computer and what you want the output voltage at.
At digikey you can find the components and hack the converter into your harness or if you search around you can find purpose made units. The are commonly used on race cars where they don't run an alternator and just need to run the ignition for a race duration. The converter keeps a constant voltage to the ignition while the battery drains during the race. After the race the charge the battery back up.
