I didn't understand it at first either. What it is is basically a chatroom service. You can create or join rooms and talk to people on them either individually or as a group. The reason we use it for RTS is because it's an easy way to find peoples' IP addresses, which you need to connect to someone.
So, if you just got Hamachi, step one is to join some networks.
Here is a great place to find that. The next step is to find someone who's on and ask them to play. Once you have that, right click on their name and say "copy IP address." Then open up RTS, say "new game," check "connect to host," and paste the IP address in that box.
The rest should be pretty clear.
