Because you're arriving from outside the Schengen area and going to a destination outside the Schengen area, yes, there will be a separate way for transit passengers. This is specifically so they can reach their outbound flights without passing through passport control.
If you are authorized, that is, if you have or do not need a visa to enter Germany, and if you have sufficient time, you can also pass through passport control and see the other parts of the airport or even go into the city. If you do that, you'll also pass through exit passport control when you go to board your flight.
If you are worried about being confused by all of this, don't be. The signs are very easy to follow to get to the appropriate part of the airport. To bypass passport control, follow the signs appropriate to your flight's gate number.