First, you make all of your monk unarmed attacks using your monk unarmed AB progression and monk unarmed damage. Then, you make all of your feral natural attacks at -5 (since they are ALL considered 2ndary to your iteratives). The Multiattack feat reduces this to -2, and Improved Multiattack further reduces this to -0.

So, a Feral Monk with a 6 BAB and Multiattack would make the following attacks.
Unarmed
+5/+5/+0 from Flurry of Blows (-1 at this point)
Feral
+3/+3 claws (net -3 from FoB and offhand)

as you advance the feral template, it would affect your attacks by giving you rend and whatnot. Those abilities only apply to attacks made with your claws, not on every attack in your full attack Flurry or otherwise.

Also, you can't have your hands full, so no monk weapons like Kamas or Sais while performing this attack routine.