Can I track CEU requirements for two licenses?

Yes.  If you have dual licensure you can add multiple license types (e.g., LMFT & LPCC) and each license may have a different renewal date.  You may apply CE hours to both licenses if the course meets all CE requirements and the subject matter relates to both scopes of practice.  CE hours must be logged separately under each license (if a course applies to both you need to log it under your first license and then log it under the second license).