Can I access two different libraries on the same computer with the remote app?

I am in the process of upgrading our home network. There is going to be an airport express in each of the main rooms of our house all running to a switch connected to our AirPort Extreme. The reason for this is so we can stream our music in any or all of the rooms we choose. I'm going to have a Windows 7 PC running iTunes constantly also connected so that we will have access to the entire library on any of our devices. My entire library will be housed on an external hard drive that will be connected to the Extreme. Here is where it gets tricky. My wife has a separate library that we want to have access to as well. It is going to be housed on a separate external hard drive connected to the Extreme via a USB hub. I don't want to combine our libraries because hers is absolute chaos and mine is very well organized. Without having to have a second computer running iTunes constantly, is there a way we can access both libraries simultaneously with the remote app? Either by running two instances of iTunes on one computer or some other way I'm not realizing. As it works right now, if we're both running iTunes on our laptops, then I can go onto my iPad and see both full libraries on the remote app. I want to do that, but with just one computer.