Hello @MacsbyCasi !

This is actually relatively easy to set up…except for the last part of your question. 

For the boxes, I think that the best idea would be to make each size box its own item (3 macaron, 5 macaron, 10 macaron….)

You could then have variations for the packaging styles. I recommend variations over modifiers for the packaging over modifiers because you can set out of stock alerts on variations.

Now the challenging part: Square doesn’t allow us to have the same modifier chosen multiple times. If someone wanted 3 vanilla and 2 strawberry in their 5 pack, there isn’t a way to do this. I haven’t heard of anyone who has made a good workaround for this yet either. You can always get creative with a massively long modifier menu of every flavor and combination, but ugh. 
I think your best bet is to have just a few modifiers (all the same, mix pack, certain flavors) then for in store sales you type in the choices in the item notes section, and for online sales, you creat an online-specific text box modifier and let them type in what they want. It’s not pretty and prone to problems with people who don’t understand, but I think it’s the best way to do it at this time. 

To create that text box modifier: open up the item in your online store dashboard, scroll to the modifier section. Add a modifier, choose text entry and follow the steps on the screen, giving it a unique name (for you, something like Which Macarons?). Now you can go into every box item and add that modifier onto the modifier list. 

I hope this helps!