why can I only have three layers: the reason is that you most likely are using the maximum dimension.
you can then only use three layers. If you would work with smaller dimensions you would get more layers.
Repositioning the selection - you can do this by pressing on the selection and moving it Or you can use the selection/transform.
Move tool - if you want to move a selected area use transform (icon that looks like a cross) - note that it can lead to minor artifacts depending on how good your selection was.
If you want to move all pixels on a layer withuot selection it will do that too.