I know you can call Biesse and they will help you out, but there a few different ways to do this.
1 - when designing small pieces in Biessworks, go to the second tab in the milling setup (additional data page) and uncheck "(ISO) ISO instruction" this will keep the small pieces from being optimised when you nest and these pieces should be cut first.
2 - (this one requires two router bits) create two router bits and set one to "rout1" and the other to "rout0". Go into the class management and set the priority of "rout0" to 3 and "rout1" to 5. When designing small pieces in Biesseworks, use "rout0" and then use "rout1" for other pieces. When optimised and run the higher priority pieces are cut first.
Again, I would call Biesse for some help. It has been a while since I programmed