It sounds like you have already gotten an answer to your question, but in case you are still struggling with this, I can describe my workflow in Fusion 360.
I try to group all of the operations that use the same endmill together in a setup, then you can click on the setup and generate a block of code for all of them at once. However, most times I have a couple of different sized endmills within one setup. So when I get to the post processor step, I select all of the operations with the same endmill and post them together. This works even if they are in different setups, you just hold Ctrl and select the tools paths you want to post together in one g code file.
Hopeful that makes sense, I’m re-reading what I wrote and can’t tell if it is clear or not. Good Luck! Learning how to use Fusion 360 seems like a never ending project, but it can do so much that is seems worth it to me.