It always starts like that.
As you discover systems shift left-click to drag them where you want them. Then be sure to go to Sys Pos [system position], and click the button on the left hand side to save your changes. There is a lock-to-grid option, also, and a way to change the size of the grid. I'm not sure what that does to a jumbled system, I always move stuff manually even when I use the grid. One bit of advice: drag the systems a good ways away, leave yourself enough room for future discoveries.