If you design the template in RGB, the PDF will generally also be in RGB. But unless you know precisely which printing press you will be using, this is the ideal way to do it. That way, the prepress operator at the print shop can do an RGB to CMYK conversion using the specific ICC profile that goes with whatever printing press they decide to use.
If you do know the precise printing press, though, there is one other alternative. You could create a PDF preset that will convert all RGB to CMYK at the time that the PDF is created. You would include the ICC profile for the printing press within the PDF preset. I know that certain DAMs have the ability to upload and specify custom PDF presets, so this could also be an option. As you may know, you can create a PDF preset from InDesign's File menu. The resulting file will have a .joboptions extension.