Leave your beer in primary for about 3 weeks total, and simple gravity should pull and solidify those flakes down into the yeast cake. Then, when you rack to your bottling bucket, be careful to rack just above the yeast cake to minimize any of that trub making it into the final product.
Primary #1 - Midnight Ryeder (Midnight Wheat and Rye)
Primary #2 - Florida Weiss
Primary #3 - Kane-DOH APA (Honey Citra APA)
Secondary #1 - Downtown Flanders Brown (brewed August 2012)
Keg #1 - Raspberry Florida Weiss
Keg #2 - Cinnamon Raisin Cider
Keg #3 - NONE!
Bottled - NONE!