Follow the transmission's manual instructions. We have a new Z12M 2.63 transmission and leave it in neutral. Plan on changing the transmission fluid at 25 hours. The transmission will hold .6 quarts of ATF, so buy 2 quarts of the same kind and you'll get 3 fluid changes with only a few ounces extra. I don' mix and match ATF brands.
Also be aware that this is not a drop in replacement for the old Kanzaki transmission. When we replaced our Kanzaki, it required a new mounting plate, new bolts, new flange, and new (longer) shift cable.