The apps/sites I use – Google Flights and Skyscanner – have a multi-city option where you can add individual legs as you need or see fit. For example recently, I searched for a return trip where I specifically wanted the outbound leg to stop over in Helsinki for 24 hours. Three flights in the multi-city option and boom.
In your case, however, you can simplify the procedure. You know that you want to fly Vienna–Warsaw–anywhere with LOT and its partners, so just go to any app or site (Skyscanner, Google Flights, etc.), select Warsaw to anywhere, set the departure time to a comfortable cushion after the Vienna–Warsaw flight arrives, preferably select LOT as the airline and off you go. Then backtrack to make sure the entire ticket from Vienna is sold as one.