"Is it possible to purchase more than one ticket via Bahn.de at the same time?"
No, AFAIK, the regular purchase process of the Bahn does not have a shopping cart. You can only purchase one ticket at a time. There is also the Bahn Ticket Shop. It has a shopping cart for multiple tickets, but it's only in German and only seems to sell tickets that you can't get online with the regular process, so it doesn't sell Bayern-Tickets.
But, what is the problem? Is the Bahn refusing to let you use the any of the credit unless you use the entire amount against a single purchase? Or is it that you don't think the balance will carry over?
I don't know if the Bahn Ticket Shop qualifies as an online purchase, but if it does, there is something called the Bayern-Böhmen-Ticket that is available from them, and you could purchase two with the cart. It costs a little more than the Bayern-Ticket (30,50€ for two people vs 27€). It works exactly like the Bayern-Ticket in Bavaria (including unlimit trasport in the MVV) but also includes a portion of the Czech Republic along the border, as far east as Pilsen.
So, you would spend 7€ more for 2 two person tickets, but you could use all of the credit (if the credit is usable at the Bahn Ticket Shop).