Hi Rachael,
Have been booking independent for getting on 20 years now in both Corfu and Turkey and only a few hiccups. The big advantage we have found is that you get the accommodation you want without the silly supplements added on by tour operators. We always have a list of things that have to be done and tick them off as done so we dont miss anything. Always book flight first, then accommodation (if you ask they can arrange the transfer though arillas is always expensive as has to be taxi cos no practical public transfer), then car hire, and finally the UK overnight stay. Have found that once the owners get to know you, they always accept payment on arrival, but initially is usual to do a bank transfer and they will give you all the bank codes you need to get you bank to do it. Be daring and give it a go and have the feeling that youve put one over on the tour operator.
Chris