It looks like you are off to a great start, here are some ideas to consider.
First, let's talk about changeover: Consider using a Server instead of the deprecated Workstation object. At the Server, you can use Task Sequences to model set-up (i.e. sequence dependent set-up), as a specific task. Take a look at the SimBit called ServerWithSequenceDependentSetup. Remember, you can access SimBits via the Support ribbon, or by finding the following directory on your machine: <C:\Users\Public\Documents\Simio\SimBits>. When you use an approach like the one above, you will see statistics about set-up reported in Results (tab) > Pivot Grid. Relevant results will be displayed, by default, at the fixed object (e.g. Server > Resource State > TimeSetup) and the changeover logic element.
About the idea of processing in batches, you might start by exploring the Combiner and Separator objects. I suggest that you look into SimBit CombineThenSeparate. In your model, you may have multiple Combiners or a single Combiner with table references. Our Combiner object requires a Parent Entity, you could consider this an order or a box for your parts/products.
I hope this information helps! Happy modeling.