You would have to match a course to the pre-req because your submitted transcripts have to 100% reflect what is in your application (or else PharmCAS will kick it back to you and tell you to make any corrections). As for telling the programs that you plan on retaking the course, that'd depend highly on what your overall application looks like and if they're willing to grant you an interview (if no other red flags with calc being the only contingency).
Some require course completion prior to summer, some require it just before matriculation after summer. You'd have to see what the rules are for each program. This would be a great reason to submit a pre-transcript application and letting someone know you plan on taking calculus for a third time.