Hello @jlvhorse ,
Nesting in Fusion was designed to handle exactly your scenario, but in a different way than you're currently trying to do it. The whole concept of a "Nest Study" was to be able to modify quantities of different parts or assemblies to see different outcomes, so for instance "3 of this assembly and 4 of this part". The idea here is that the quantities of the individual parts of an assembly is determined by the Bill of Materials of that assembly. Fusion doesn't have a formal Bill of Materials, but it does have quantities of components, and that's what we use to determine how many of an individual part are considered to be in a particular assembly.
Anyway, the quantity you see on the Nest Study UI is really the quantity of the highest-level assemblies being nested. You wanted to combine parts from different documents and nest them together, but combined them yourself into a single document. In doing so, you effectively created an assembly, the quantity for each part being 1.
So there are two ways of looking at this situation. Either the parts are really part of an assembly, in which case you actually want to create more instances of the part to reflect how many are actually in that assembly, or you really want to treat the parts separately, in which case you don't want to create an assembly in the first place.
The second case, treating the parts separately, is done via the Component Sources command, which allows you to combine one or several documents into a single manufacturing environment.

When you add models from other documents in this way, you will see multiple entries in the "Nest Study" dialog when you choose "Multi-value" for "Job Quantity":

This makes it possible to combine completely unrelated assemblies and/or parts into a single manufacturing document to achieve more optimal material usage, since there are more possibilities for the nesting engine to try. This is precisely the reason why the "Nest Study" concept exists, and why we provided the "Component Sources" functionality in the first place.
Phillip Doup Architect - Fusion Platform UI