The 5MB size is per APP. So it depends on the tables/sheets your app uses and would be independent of the source. By the way, there is some mention of increasing the size in the documentation. Not sure if it was increased
As for design, using multiple sheets versus multiple workbooks, for me this depends on the future of your app.
I am building apps small but hope they grow into larger systems. Because of this I think of the sheets as relational database tables and the workbooks as databases. I try to use database standards and avoid using formulas in my sheets. Why? Because if the client needs to grow into a larger system with a relational database, I can easily export the sheets and import them into an SQL database with very little effort and virtually no changes in the app.
However, if you expect your app to never need a relational database or system, then I would keep it in one workbook. It is easier to manage. There are exceptions which you will certainly know when you encounter them. For example you might find the users needing or wanting access to some of the raw data. In this case, I would split that data into a separate workbook and give the users access to only that workbook.
There are other exception scenarios but you will know when you encounter them.
Hope this helps!!
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