Omega 6 itself isn't bad for your dog. It's the imbalance of omega 6 to omega 3's that are bad - and the process of manufacturing kibble creates that imbalance. Omega 6's are an essential fatty acid, just like omega 3 but when the dog is getting way more omega 6 and not enough omega 3, it can cause problems. Brewer's yeast is considered to be a form of probiotic, but considering that the manufacturing process would destroy any good bacteria anyway, there are better sources out there.
What I do on dog food is to research what the ingredients really are - not whether someone says they are bad or not, just what they are exactly. Then I decide if this ingredient is something I want my dog to have. I make a list of the things that I do want them to have, the things that I can live with, and the things that I absolutely do not want in their food at all, ever. Then I find a food that meets my requirements.
Oh, and I forgot to add that your dog might be having runny stools because he's getting too much of the new food. With a higher quality food, you don't have to feed as much because the dog is actually absorbing the nutrients in the food rather than ingesting huge amounts of low quality food to get the nutrients they need and letting the rest continue out the other end. Also, IMO the suggested feeding amounts on the higher quality foods are high. I think my food suggests feeding like 5-6 cups a day for my newfie girl, but in fact she only gets 2 cups of dry and 1/2 can of Evanger's 'Hunk of Beef' per day - and she's doing wonderfully.
Livin in a Newfie Drool Zone