Hiya,
We're also doing a multi-centre honeymoon. We booked our flights for our honeymoon through Travelocity.com. Don't know if we could've got our flights cheaper elsewhere or not, but they give lots of options for most routes within the iteniary.
You can tick a box if you prefer non-stop flight over cheaper etc and they will show the direct flights first, if available. or you can choose to go with one airline if you want to go that route. We're going with different operators all the time, but all our flights are direct so we don't have to worry abut connecting flights etc.
They don't seem to work with just the main operators also, as one of the shorter journeys we're taking is with a company called Jetblue Airways. They're like the US equivalent of RyanAir, but have a whole new fleet of planes with indiviual TV screens etc so presumably budget airlines in the US are not quite the budget we're used to.
HTH.