There seems to be a little confusion here, a CAP 509 Course was an ab-initio course from zero to CPL/IR in 12 months. These courses ceased in 1999 and have been replaced with the JAR-FCL Integrated Course.
If you already have Commercial licences neither of these courses are relevant to you.
The JAR-FCL ATPL is designed for Airline pilots not for GA pilots. The idea is that you fly as First Officer with a CPL/IR and after 500 hours as a first officer you can apply for an ATPL. If you don't fly multi-pilot aeroplanes you don't need an ATPL. You only need to have passed ATPL exams and hold a CPL/IR to get a job as a First Officer.