Issue with Photos initial import

So I have two different iPhoto libraries, a main library, and a smaller ancillary library on another mac. I upgraded both yesterday to the latest version of OSX, which included the new Photos app. However, the ancillary library synced with iCloud before the main library had a chance to. Is there anyway to change the main library that syncs to iCloud to my other iPhoto library? At this point, all I can see in the Photos app in iCloud is the 10-15 pictures that were in the ancillary library.

Any help would be appreciated, thanks.