You do what every company that has to follow GAAP on top of other accounting rules does, two books, properly audited and bridged. Maybe that stuff isn't straight forward for everyone, it is for pros in the field. It serves to have those pros do these jobs for you. Like, you know, a professional company.

And yes, using the correct software suits and processes, intra EU VAT is straight forward and done by litteraly thousands of small businesses every single day. And then there is the less straight forward aspect around optimizing taxes and VAT. But that last bit seems not to be the problem here, is it?