Gucci - I posted this on another thread but just in case you haven't read it here it is.
The difference is that schools approved to run the JAR ATPL do the full integrated course, including all the written exams and 195 hours flying. Schools approved to conduct training for the JAA CPL can do so for the modular CPL course (25 hours flying).
For example: OATS, BAe, Cabair and WMU are approved to conduct training for the JAR ATPL course.
Professional Air Training, Multiflight etc. are not approved to conduct the approved ATPL course. Instead, they have approval to conduct each flying module. Both ways get you the same licence in the end.