"Does anybody have any suggestion where to start the trip ?"
Amsterdam's at one end of this line-up, Salzburg and nearby Munich at the other. Maybe AMS or MUC? Fly out of the other.
"What should be the itinerary?"
It's pretty much a straight line, so order should be no issue. How many nights in each place? Well, since you picked these destinations with some ideas in mind about what you want to see and do, you should probably decide that.
"We are planning to do the trip by car."
I would probably want to avoid Cologne, Amsterdam, Munich, and perhaps Salzburg as well. Parking is a hassle and fees add up. Also, if you rent in one country and drop in another you'll pay a heavy drop-off fee.
I would absolutely do this trip by train. Check DB prices for your travel dates for all journeys. A'dam - Cologne can be purchased for €19. Cologne - Munich can run as little as €39, maybe €20-€30 more, depending on when you purchase them (best prices are always 91 days in advance when they first go on sale.)
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