If you have an Global Pass, it should work. Which pass did you have buy? 

All trains that you have listed are included in the Interrail Global Pass. 

For the Nightjet/Euronight Bologna-Munich you need a reservation (it starts from 14€ for a seat). You can buy it online via tickets.oebb.at (select the discount “Interrail/Eurrail - Globalpass”) or at Trenitalia ticket office. You will use only one travel day (if you haven an flexi pass) for this trip and an outbound journey. 

For the train munich - prague, only hop on. No reservation needed. 

From Berlin to Amsterdam, there is no direct night train. You can use night IC and ICE (reservation not obligatory, you can book one via bahn.de for 4€/trip), but please note, that if you change trains after midnight you need with an flexi pass a new travel day. 

From Amsterdam to Paris you can use Thalys high speed trains for 35€ reservation/person. You can book it via interrail.eu reservation service with an additional fee. 

From Paris to Bologna there is no night train. You can use daytime TGV (ca. 30€ reservation) to Milano P.G., and than change to a Regionale Veloce to Bologna or Frecciarossa (10€ reservation). 

Maybe is it cheaper to buy a normal ticket for the new Frecciarossa Paris GDL - Milano C.le. Interrail is not valid. 

Or you can use the Nightjet from Paris to Munich (from 14€ seat reservation) and change there for the Eurocity Bologna (10€ fee, reservation not mandatory).