i think what the CIA is doing is funding ISIS to get AQAP jealous, in hopes of having a full scale war Dirka Dirka war between the two groups.
the CIA funds and directs both groups to do the jobs they cannot politically do and with the rise of ISIS, Al Qaeda is going to feel left out. they should begin to bring the heat and try to get their name in the spotlight or, which i find highly unlikely, they will enjoy the attention ISIS is getting so they can go under the radar. but with both groups, the real important thing is name recognition to all the other idiot Dirka Dirkas.