I had thought Kayak was a metasearch product and searched airline sites on your behalf, but maybe that's changed in significant time since I was involved in online travel.
Either way, search how you like, but you'll almost always get better exception service if you are booked directly with the service provider than if you're booked as a 3rd party customer or a code share. For airfare, costs are usually similar or even a little less expensive if you book directly; for hotels, there are times where the prices are significantly different, but you may be able to get the hotel to match prices if you call them to book directly.
Exceptions would be if you have a high value relationship with a corporate travel agent, or maybe a high level amex?
If you book through an online travel agent and something goes wrong, chances are the provider will send you to the travel agent's customer support and they will be slow and may not be able to do much, because they don't have the right access.
Either way, search how you like, but you'll almost always get better exception service if you are booked directly with the service provider than if you're booked as a 3rd party customer or a code share. For airfare, costs are usually similar or even a little less expensive if you book directly; for hotels, there are times where the prices are significantly different, but you may be able to get the hotel to match prices if you call them to book directly.
Exceptions would be if you have a high value relationship with a corporate travel agent, or maybe a high level amex?
If you book through an online travel agent and something goes wrong, chances are the provider will send you to the travel agent's customer support and they will be slow and may not be able to do much, because they don't have the right access.