Plants will help the cycling eventually by sucking up nitrate, so chuck em all in
There are a number of ways to start, I tend to fill it up part way like you suggest, add plants and then fill it up further. Some have planted them out dry in the soil but kept them moist (bit too complicated for me) and some just fill up the tank and then add the plants. It's certainly easier to see how they are going to stand in the water if there is enough to cover them. You just have to be a bit careful so as not to stir the bottom up too much when planting.