Travel strategy before and after Best of Adriatic tour

We booked through United and flew Sacramento to Dulles to Munich to Ljubljana. It was an exhausting day. We enjoyed Ljubljana and I would have spent some more time if I had known what a pleasant place it was. At the end of the tour we rented a car in Dubrovnik and drove to Dobrota Montenegro, just outside of Kotor where we rented a flat through VRBO. We spent a delightful week exploring this part of Montenegro. After our week we returned the car in Dubrovnik, overnighted then flew home, once again on United to Munich, Chicago, Sacramento. Our flights were all listed as United or Lufthansa but the last leg into Ljubljana was operated by Adria. OK flight, don’t eat the food.

The only small airlines we have used in Europe is Ryan Air. It is an okay airline and cheap for short flights. The airfare starts low and can quickly add up so be careful. We paid for priority getting through security and there was no priority getting through security. I would pay for a reserved seat, because sometimes these flights get overbooked. It is fun, consider it an adventure.

we will probably fly in and out of the same city (that seems cheaper than 2 one-ways).

Two one way tickets would be the most costly.

Do not overlook 'multicity' ( aka open jaw) tickets. Fly into one city and out another on a single booking. Quite often these are the same or very little more than a round trip ticket and save you the bother and expense to get back to where you started from.

As above, book airline tickets as multi-city not two one ways.
There are many excellent smaller airlines , many of them budget, in Europe. Check on both Skyscanner and Google Flights to see what is available in and out of those cities.

We're taking that tour this summer. Flying round trip San Francisco to Zagreb and using train
to get to Ljubljana and small airline to return to Zagreb from Dubrovnik. Hope it works.

I flew Amsterdam to Zagreb via Croatian Airlines (codeshare with KLM), spent 2 days there visiting some great museums and walking tours, then took the train to Ljubljana. Croatian Airlines is a smaller airline, but with modern 737s (or Airbus equivalent), and the service was fine. After Dubrovnik, I hired a driver to Sarajevo, spent 2 days there (very worthwhile if you have any interest in history), then took a public bus to Zagreb, before flying back to Amsterdam via Croatian Airlines. I had some skepticism about CA, in part because I couldn’t pre-select my seat, but they operate more like a “regular” airline than a budget (nickel-and-dime you to death) airline, and the connections with KLM were super easy. CA’s code-sharing with KLM sold me, and I thought Zagreb was a great addition to the Best of the Adriatic itinerary. I think Croatian Airlines also flies from Dubrovnik directly to Zagreb (and even from Sarajevo to Zagreb).

You don't book two one-way tickets. You book multi-city commonly called open-jaw. We book most of our trips open jaw and rarely find them more expensive and especially if you add in the time and expensive of returning to your original site, open jaw will be cheaper. There is some risk if you book two separate tickets -- into Amsterdam and then on to Dubrovnik. I would try to book a single ticket to your final destination. That way you are covered if something goes wrong on any of your flights. It is smarter and much less stressful. Good luck.

Similar to Frank's point: Your open-jaw travel plan also need not transfer at the same city in each direction. Search to/from your actual destinations, not just to Amsterdam, and not planning separate, unprotected connections on unrelated carriers.

For instance Delta/KLM and their partners should be able to get you to/from almost anywhere with one connection, and so should the other major airlines and partner groups, like Lufthansa via Frankfurt. If you're a lover of Alaska Airlines miles (no longer working with Delta/KLM), then look at their partners Aer Lingus, Condor, or American/British Airways.