A CPL is a CPL, it has nothing to do with single or multi engines. However, you can do the CPL test in a multi engined aircraft and at the same time get a MEP (multi engine piston) rating.
For the fATPL you need a multi engine IR and a CPL. You could get a SE CPL or a ME CPL first, the final result would be the same. Some people do a SE CPL because they think it's cheaper, others do the ME CPL either because they think it looks better on a CV (very little difference IMHO) or because any ME time is good and it helps prepare you for the extra workload of the ME IR. To me that's a good reason to do the ME CPL.
Either way, you'll have a SEP rating already. You don't have to do SE and ME CPL.
That is my understanding of JAR / EU Ops