The article is a couple years old, but describes the Pentagon vs CIA situation in Syria:

"Last year, the Pentagon helped create a new military coalition, the Syrian Democratic Forces. The goal was to arm the group and prepare it to take territory away from the Islamic State in eastern Syria and to provide information for U.S. airstrikes.

The CIA, meanwhile, has its own operations center inside Turkey from which it has been directing aid to rebel groups in Syria, providing them with TOW antitank missiles from Saudi Arabian weapons stockpiles.

While the Pentagon's actions are part of an overt effort by the U.S. and its allies against Islamic State, the CIA's backing of militias is part of a separate covert U.S. effort aimed at keeping pressure on the Assad government in hopes of prodding the Syrian leader to the negotiating table."

latimes.com/world/middleeast/la-fg-cia-pentagon-isis-20160327-story.html