If you're flying to multiple destinations it matters which destination you visit first, which one second and so forth. SkySave tells you which route is the cheapest. For example, it can be a lot cheaper to fly London -> New York -> Miami -> Los Angeles -> London than if you were to go to LA first and then Miami. Does that make more sense?

OK, that really wasn't clear, so here are some specific suggestions:

The video under the white text often makes it difficult to read the catchphrase. I'd suggest editing the video to reduce the brightness by 60% (No doubt others will disagree);

The text at the top does not, to me, communicate this idea that you are choosing multiple destinations, and that the site will try all the orderings to find the optimal itinerary;

It says:

Discover the cheapest route to fly for your next holiday

You are using the word "route" in a way that doesn't communicate to me the idea you've mentioned above;

It says:

If you're visiting multiple destinations it can be on average 30% cheaper to fly a specific route as opposed to others

Again, you're using the word "route" in a very odd way.

So, concrete suggestion to highlight the problem, I'd say something like:

You choose the places to visit - we'll arrange your itinerary to minimise the costs.

I found it hard to put it succinctly but I quite like your description. Might use that instead!