Odd you don't see each other. That might be a bug.
My friend that started last night invited me to a group and I gave him a tour of the Starbase showed him where to find things. As long as your in a group you guys shouldn't have a problem joining the same instance of a zone. At least I haven't had that problem yet.
There is only one server, however each zone is split into instances. So for example: your normal sector space zone instance houses up to 75 different players. The next 75 would end up in another instance of that same space.
If you end up in Sol System 1, your friend may end up in Sol 2 and while all your surroundings look the same, the contained players will be different. You can switch "instances" by clicking on the name above the minimap and finding the one your friend is in. You can coordinate your locations from there.
OK, I dont know how we did it but 45 minutes of fiddling arround, we managed to get at the same spot. I found the instance button, clicked it, and while trying to see where we both were, the game automatically, put us in the right spot. It did it semi automatically, while browsing we both warped to the same server <i guess>