There are different ways of sync'ing libraries. You can merge them, which is what you want to avoid, as you have different content on different libraries, or you can just make each separately available through your wireless setup, to every playpoint in the house (your laptop, the mini, the ATV ...) The instructions for choosing modes are quite straightforward.
In my home, I have a number of outlet points, either computers or Airport Express units. Using the laptop or the Touch/iPhone, I can select a library, content from the same, and then choose which outlet I want that music piped to, wirelessly. It's quite neat. As you already have a server, you'll just assign that as your main depository for the content you put into your system from the mini, and don't let yourself be constrained by the capacity of the harddisk on the mini. I keep very little content on it, and have the majority on a stand-alone NAS-server.