Cheap flights within Europe

I recommend you take a look here:

skyscanner.com

and here:

whichbudget.com

You have the choice of https://www.airdolomiti.eu/ or https://www.airdolomiti.eu/

If you don't get the price or times you want flying out of Bologna, look into flights out of Florence.

There is also a direct overnight train from Bologna to Munich, although the departure is a bit late (22:46). That is probably the cheapest way as it saves you one hotel night.

Many cheap airlines like Skyscanner works within Europe. Yes, Skyscanner offers fewer fairs for within Europe operations. EuroCheapo is another airline that works with reasonable rates and yes also accommodate with hotel and car reservation. You can also check the fairs of different flights. Or even can try Google flights option. Another option that I can suggest you is Cheapoair. Yes, you can try this for within budget flights.

Beware the post immediately above mine. CheapoAir has been the subject of a lot of serious online complaints, and the poster seems not even to realize that Skyscanner is not itself an airline.

Skyscanner is often recommended as a good source of schedules and fares. I can't imagine booking a budget-airline intra-European flight anywhere other than the airline's website.

I am not saying to reserve flight other than official website of the airline. I am only recommending to check rates and offers of different airlines from one point to your destination. Don't misunderstand it.

My apologies if I misinterpreted your intentions.

I use Wikipedia to check what non-stop flights are available out of airports all over the world. Someone in the industry maintains the listings. The biggest airline going into Bologna is Ryanair.
But the only airline flying from Bologna to Munich is Air Dolomiti.

I use skyscanner a lot, and I understand that it is a go-between which, for the most part, doesn't sell tickets. Rather, it provides links to sites that do, including the airlines themselves. I have yet to find a website service that covers as many inter-European routes. Transcontinental is a different story.

Wikipedia is a good place to find routes, just be aware that there might be old information in the articles, even if they are surprisingly accurate. Another good place is https://www.flightconnections.com/ that is very userfriendly, and seems pretty accurate at least.