How do I properly substitute flour and water for sourdough starter? I have a sourdough bread recipe that I want to try. The recipe calls for 2 cups starter but I do not have that much. It says I can use less and to just make up the difference with equal parts flour and water. If I use 1 cup of starter does that mean I use 1/2 cup of flour and 1/2 cup water? or 1 cup flour and 1 cup water? 

This is my first sourdough bread attempt and I don't want to waste my starter with a stupid mistake. I have worked too hard at keeping my starter alive to mess it up now.
Starters are typically maintained at 100% hydration.   That means equal parts water and flour.  So, in your case, mix equal parts water and flour.  Measure 1 cup of that, and add it to your mix.  Of course, this will mean that all of your starter is gone.  Alternately, feed your starter (equal parts water and flour) with more than you need, and let it sit on counter over night.  Then you you can save the left over to use again next time.