What about the submissions ?

What about the submissions ?
Are they stored all in the same Table (the one for the main form) ? or in two differents table, one for paypal and the other for Purchase order ?

Yes, that is correct. Since you will be using two forms, the submissions will be on separate tables as well - one for each form.

But you can add data to a table from another table. Here's a guide for that: https://www.jotform.com/help/1002-how-to-get-data-from-other-forms-in-jotform-tables.