We probably should as a minimum allow you to customize what the 'Company Registration Number' and 'VAT Registration Number' are called, as I know this is an issue for other countries too. We'll work on that.
You could always add IC=xxx and DIC=xxx to your Invoice Comments for now. Each invoice you create after that will include these comments by default.
We are working hard on producing some invoice templates for you to choose from. The next step will be to allow you to create your own, probably based on CSS styles for the time being.
I'm not sure that will give you the language flexibility you need, though. Of course, if you help us get enough Czech users, we'll produce a localized version just for you ;->
EMPLOYEE