It is useful to understand the differences between a rating and a licence.
The CPL is a licence.
SEP is a rating
MEP is a rating
IR is a rating
Once you have a base licence, it is valid for any aircraft type you hold a rating for. If you do a multi engine rating and (keeping it current) 5 year later do a CPL in a single engine aircraft, you will have CPL privileges on multi engine aircraft. (True for JAA, not sure how it works in other countries, I think it is different in FAA land).
As the IR is a rating, there is a difference between doing it on a SE or ME aircraft, as doing it in a SE will allow usage only in SE aircraft, whereas doing it in an ME aircraft will allow you to use it in both SE and ME aircraft.
when you see the "Multi Engine CPL" advertised like on PAT's website, what you will actually be training for is a CPL and a Multi engine rating.