Can I Assign an Athlete Two Programs at the Same Time? Say at Mon/Wed/Fri Strength Program and a Tues/Thur Conditioning Program?

No.  

You cannot create two programs that have “interlocking” dates where Program A is Mon/Wed/Fri, and Program B is Tue/Thurs.  A program is simply a collection of connected dates.  If you have a standard Monday (as example, for Strength), copy this day and save it to the next Monday.  If you have built out a standard Tuesday (as example, for Conditioning), copy this Tuesday and save it to the next Tuesday and then make any modifications to that Tuesday.  Use circuits as re-usable block of exercises to speed up building these days.