It's always difficult to set out the 'best route'. Lots of it depends on what you want to do and see. You have 6 weeks. That's plenty of time if you cover 1 or 2 countries, let's say Ecuador and Peru. It's not for 4 countries, you'll be rushing all the time. Spend as much time as you can in the Andean countries (Ecuador, Peru and Bolivia).
Write down highlights you'd like to see and start from there. I have a free e-book to get you started:
Attractions of South America