Cannot choose a folder to import specific photos from Photos to my iPhone through iTunes

I used to sync with Aperture but since updating to El Capitan and Photos I am having a problem. I import my pictures from my iPhone to Photos but also like to sync a few other specific photos that I had made an album for in Aperture. Currently these are there but I now would like to create another album of photos that are on my iMac in Photos. Although I have not checked Sync Photos in iTunes I can see that the greyed out selection is a folder called Pictures. If I check the sync box and then look at the drop down menu Pictures appears to be a folder in my user account that contains two greyed out items (Photos Library and Photo Booth Library) and another folder called Aperture Slideshows. This Aperture Slideshows folder is empty and I cannot select the greyed out icons. Even if I select to sync All folders it stays on this same file list. I store my photos on an external drive and if I choose that drive from the Finder I can see the Photos Library inside the Pictures folder perfectly well. If I try to change the destination from within iTunes however I am not seeing the same options.