I wanted to update everyone, I was mistaken. I played with it a lot a kept a paper log (since my memory isn't great) and it does appear that it is only counting when the engine is on. I just can't believe in 2 months I have put over 50 hours on the engine.
Sorry for the noobie question and thanks for everyones reply. I am loving the boat and the community. If anyone is in the Nashville area and get out on Percy Priest feel free to send me a PM. I would love to meet some new friends and hopefully learn a lot.