I'm going to chime in here because this thread is relevant to my interests. My wife and I both work from home and have for over 2 years. She works for a small insurance company and has a pretty demanding job that keeps her very busy. We have separate offices that are not within ear shot of each other, which I think is a must. Before we had kids, we would both be in our offices most of the day, and we tried not to bother each other very often, so we could both be productive. This worked very well for us and we never had any issues. Now that we have 2 kids, I'll usually watch them in the mornings while she deals with her East Coast clients, and then I'll get some work done in the afternoon. We both respect the fact that each of us has a job to do, so we are mindful of that when the other is trying to get shit done.
If both of you are going to be working from home doing different jobs then I think having your own separate spaces is a must. If you need to contact each other during your work hours, use skype or an IM so you don't have to get up and walk to the others office. Sounds stupid but nothing destroys your workflow like leaving your desk to go ask her a question or vice versa. Have lunch together during the day or go out to lunch for a break from the house. Getting away from the house for some personal time will be even more important if you're both working at home. Even if you guys are doing your own work most of the day without too much contact, it will still start to feel like you don't have any personal time for yourself, so make sure to get out a couple times a week to do whatever you like to do.
All that being said, my wife and I were married for nearly 8 years before we both started working from home, so we had and have a very strong relationship. I can't say for certain how this would work with a girlfriend, but I dont' see any reason you can't give it a try and see how it goes.