Field Not Showing in Process Builder

I tried this and saw my checkbox field no problem, so I'm going to hazard a guess that you have fallen into the "Select a Field" overlay trap. Which is this:

When you click on the "Object" field and it gives you the "Select a Field" overlay, it's REALLY asking you to select an object, not a field. So it gives you a list of lookup fields to navigate to a related object.

If you click on the object name, and click save, it will then give you a list of fields on that object that you can update.