Assuming your school does not use Naviance:
You do still have to invite your recommenders and assign your recommenders to schools electronically through the common app process, even if they will be mailing their recommendations.
Separate from your actions, each recommender has the option (upon receiving the emailed invitation from the common ap) to submit all recommendations for all students during this entire application season either by email or by regular mail. (A recommender cannot elect to submit some recommendations through the common app electronically and others by mail.)
You don't do anything differently in your common application submission regardless of how your recommender will be submitting the rec. (However, you may want to provide stamped addressed envelopes to the teacher if he or she will be mailing them.)