If you get the FAA CPL as part of a JAA fATPL course, it will not matter to a future employer.
But as has been said on this forum, it is best to use a maximum of 2 flight training providers.
You will find the FAA ratings easier to obtain, and in some countries preferred to JAA ratings.
Getting both ATP and fATPL ratings may in the future enhance your job prospects, but that might be in the distant future when the market improves.
Should you live in Europe and intend to remain there then go for the JAA fATPL, without it you will not get a job.