With respect to any of InDesign's drawing tools, you may set Fill and Stroke colors before choosing the tool. There are several ways to approach it:
1. The Tool panel: Click the Fill well or the Stroke square in the Fill/Stroke proxy at the bottom of the Tools panel to bring the desired element to the front, then set the desired color of that element by:
- Clicking a Swatch in the Swatches panel
- Setting values in the Color panel
- Choosing the Eyedropper tool and clicking an existing object
2. The Swatches panel: Click the Fill well or the Stroke square in the Fill/Stroke proxy at the top of the Swatches panel to bring the desired element to the front, then set the desired color of that element by clicking a Swatch.
3. The Color panel: Click the Fill well or the Stroke square in the Fill/Stroke proxy at the top of the Color panel to bring the desired element to the front, then set the desired color of that element by setting the desired color values
After that, if you choose the Pen (or any drawing) tool, you'll be drawing with the Fill and Stroke colors you pre-set. In this way, InDesign's drawing tools "default" to the pre-existing Fill and Stroke colors in effect when the tool is chosen. There is, however, a "global" default Fill and Stroke of None and Black respectively, and to can revert to that at any time by tapping the D key with nothing selected.