My Yorkie also had problems on Royal Canine. She would have eye goop and itchy skin. Once I switched the eye goop stopped as did the constant scratching.
You may want to consider a grain free kibble. Often when a dog has issues with kibble it's because of a grain within the kibble. I'm not familiar with the Holistic your are feeding. It may very well be grain free.
As for the runny poop...could this be because you switched his food to the Holistic? If it wasn't introduced gradually (mixed with whatever he was eating) then it will often cause loose stools.
There are wonderful threads and stickies on here regarding food with links to internet sites that grade all the high end foods. Be prepared for information overload!
Good luck!