Hi Corinne, as I recall we added a mixture of caramelized onions and poppy seeds to the Onion Rye at Zingerman's; something similar to the filling we use in our bialy recipe. I would recommend adding a small amount of caramelized onion mixture at the end of the kneading process on low speed, which is generally when I try to work in ingredients that are likely to disrupt gluten development. You can also sprinkle some of this onion mixture on top of the loaf prior to baking. It will take some experimentation to find the exact right amount that works well with this recipe, but I would start on the small side (maybe 1/4-1/3 of a cup) and go from there. I hope this works well for you! Let me know how it goes. 

Barb

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