You can use the theory credits for CPL, or IR or both.
Doing the CPL only is an option, albeit a strange option as the IR requires fewer hours than the CPL and should therefore be done first. Technically you could do the CPL then the IR via CBIR at a later date and still get an airline job (the ATPL exams are required for first MP TR but I don't think there's an expiry date for that purpose)