As a regiment from the Prussian estates you'd fight, historically, on the side of the Polish-Lithuanian Commonwealth. The Duchy of Prussia lay outside of the Holy Roman Empire but was ruled by Brandenburg. During the Second Northern War, which is when the Deluge takes place, Frederick William I of Brandenburg-Prussia entered into an agreement with the Polish king to supply a large number of men to fight against Sweden, including 1,500 infantry from the Prussian estates. It wasn't until the 1660s onwards that Prussia started to gain power and to forge it's own path. In 1701 Prussia was elevated to be a Kingdom under Frederick III.
Unless, of course, you decided to be a group of Prussians who don't like Poland and instead choose to fight for Sweden.