My guess is the 55amp alternator will provide more amps than the winky charging system on the 9.9hp kicker.
Frankly, it depends on how much current is being drawn by the various electrical components on your boat and how long your engine(s) are being run. An engine's alternator will only deliver the amperage required by the electrical system to keep it's batteries fully charged (approx 13.6 V).
At the simplest, when you're trolling on your kicker with its 12 amp alternator and your stereo, GPS, down riggers, etc are only drawing 12 amps, the kicker will be sufficient to keep your batteries charged. If you were running on your main engine and drawing the same amperage, your main engine's alternator would only deliver 12 of it's potential 65 amps to the batteries.
Another way to look at it is your trolling motor will produce 12 amps in an hour, while your main engine might produce 65 amps in an hour. So 5 hours running your troller will produce almost as much as one hour running your main engine.
So yes, the 65 amp alternator will provide more amps than the "windy" charging system on the 9.9 kicker but only when the two engines are run for the same time period. Typically, though, we run our main engines for short periods of time compared to the hours we use our kickers for. So that on a typical fishing trip, it could well be that the "windy" kicker is delivering as least as much average to the electrical system as the "not so windy" main engine alternator.