Been there. It can be really challenging watching your SO fall in love with another person. I think that's why a lot of people develop individual relationships instead of going for the Olympics of a triad/threesome right away. It puts all of the challenges of poly right up front and personal in a very spectator-sport kind of way.
I went through similar feelings with my husband and his now ex-girlfriend. We started out as a triad, and they developed a stronger emotional relationship after just a few short weeks. It took them longer to realize that they needed alone time than it did for me to see the need for it, but none of us were really willing to make the call.
It sounds like when you're occupied with someone else, and outside of your home it is easier for you. Perhaps when they have one-on-one time it should be at her place, and you should have other people to hang out with - whether it be her mom, a close friend, your family, or another partner of your own. This will enable you to not be immersed in their NRE, and not have it be so in-your-face.
Kudos for you for being honest with yourself about your feelings. I find that it helps to dissect jealousy, as underneath that blanket/umbrella feeling, there are other issues that you can take a look at. Remember that while it is a valid feeling, it is in fact just a feeling, and doesn't necessarily make the fears, insecurities, anger, etc. legitimate outside of being a real feeling. It can be a construct of past insecurities, a fear of abandonment, or other "ghost emotions" that really hold no basis in reality when you look good and hard at them outside of the immediate situation.
I found having coping strategies helpful - had friends I could talk to, journalled, went for jogs, did yoga, blogged, cleaned the house, had a mantra that I recorded and would listen to, got a life coach, etc. When you make those feelings your responsibility, and find positive ways of approaching them it gives you activities that you can turn to that will improve the quality of your life, which in turn makes it easier to deal with the feelings.
I think it's important to share your feelings with both of them, and ask for what you need, as well. What do you think you need to feel safer and more at ease with their connection? What do you think would help you when you're feeling that way so that you don't feel that you have to hide away and be sad by yourself? I know that feeling, and I can tell you from experience that it a) doesn't make you feel good b) doesn't make the situation better. I would encourage you to find ways to express yourself, and take care of yourself during those times so that you can tackle those tricky feelings without being alienated.