There is no problem in an ATO quoting a separate fee for each course or a single fee to cover both courses. Bear in mind that only the 6 hrs training for the MEP is required to be completed before commencing the CPL(A) flight training (i.e. there is no requirement for the skill test to be passed or for issue of the rating). The important thing is that all of the MEP training must be completed before the CPL(A) course flight training is commenced. It is not permitted, for example, to complete the SE element of the CPL course, then the MEP training, then the ME element of the CPL course.