It might be important to note that, at this point, we're not so much interested in how much we make from the actual booking as much as we're interested in the conversion rate itself. We use the Expedia & SkyScanner APIs, which was more practical from a technical perspective to get to MVP as soon as possible. But the affiliate fees for flights are close to nothing ($2 if we're lucky) and we have different solutions in mind.
We only ask for the user to sign-up once she clicks the 'save itinerary' button, which we believed would be the most seamless. The most confusing part of the product so far has been the fact that we currently have two 'book now' buttons once the user tries to book her flight, something we're addressing.