Heya!
Firstly, I applaud you on approaching this in a positive manner. Researching and discussing this with your partner is the best way to start. Developing an understanding as to what she's going through and empathize with how she feels may help you come to terms with this.
But remember -
they are still the same person you fell in love with; you want to be with; you want to start a family with. Outwardly, they may change, but inside it remains the same person - though hopefully more comfortable in their own body and no longer feeling depressed by circumstance.
First things first, I'd seriously recommend getting in touch with a therapist, preferably one specializing in gender issues. Having someone knowledgeable and experienced in similar cases can help your partner shift through the emotions and make sense of the jumble of desires in their head. It'll also give you valuable information, resources and purpose.
If you want kids, then you should also consider banking sperm.
Also, having you as a pillar, as a support, will be immensely helpful to your partner. She's going through a turbulent period of emotions and intense feelings, so having a constant in her life who has her back, and will love her no matter what, will be invaluable.
If you feel a bit overwhelmed or lacking in information, there are plenty of "Partner-of-Trans*" -type support groups and resources out there.
Some people accept transsexuals, some don't. But think what's more important - the outdated opinions of the narrow-minded, or the self-happiness of the person you profess to love?
Erm ... I think I've covered most things

Anything else, then fire away!
x