Out of interest, if I book the flights and hotel through the same company, but they decide to use different airlines for the connections, whats the situation with regards to a connecting flight being missed due to delays further back? Is there any protection, or is it 'unlucky sunshine' and probably some sort of admin charge to get on the next flight ?
I believe if the flights are issued under the same itinerary (e.g., booked through a single airline even if there is a partner airline involved for the connection) then they are liable to make good if a connection is missed due to the first flight arriving late. This would likely be a case of providing food/drink at the airport and providing overnight accommodation if the next flight isn't until the next day. If the flights are booked separately you'd be looking at goodwill as the airline isn't deemed to have responsibility for your ability to complete the entire trip from origin to final destination.
Make sure you have a good shop around before just booking the whole lot through an agent.
As well as sky scanner take a look at these (expect you'll likely get the same results, but always worth checking!)
http://matrix.itasoftware.com
http://www.kayak.com