The one on the left will show the current system map with all of the units, planets, resources and other info that you can usually find in any RTS map. The second of the mini-maps will show the connections between the various systems and the systems themselves. Once you have discovered a new system by finding a wormhole, you'll be able to switch to that system by clicking on the dot that represents it. Once there, the system map will change to current selected system so you can see what's going on there. Actually controlling the jump points will be one of the major tasks for all wannabe generals and where you'll probably see most of the big battles raging.
Players can take control of a warp point by building a warp gate over the top of it.
This means that only your troops will be able to make it though to the other side. Any opposing player needing to get to the other side will have to destroy the gate before that can happen. All that being said, it seems as though the task of controlling all of the different systems would be a pretty difficult thing. Well, that's not an entirely mistaken thought, but there are some measures that the developers are taking to help people out with this a bit. The first and foremost of these being the creation of admirals.