Yeah booking flights is a pain the ass! The prices you see advertised on websites like kayak and skyscanner only existed at one time, say 6 months ago, they can still advertise the flight at that price because they write 'from' in small letters at the side of it! It doesn't seem to matter that the price they are quoting doesn't actually exist anymore. Some places add the extras at checkout like tax, booking fees, admin costs & baggage allowance.
Flight Centre are good because they can see and tell you the real prices, in real time, for all flights/airlines. Also, if you ring up and they give you a price, you can have them hold it for a few hours, booked under your name, whilst you make your decision.
When I booked, the flight I was looking at was changing constantly from £457 to £539+ the booking agent said when more people search for the same flight online, the price moves according to demand, so it's best to ring up and get a live price. I'm sure I drove the booking agent a bit mad, I kept sending screen grabs going 'look, it's changed again!'
Also it is good to check the airline's website for their price - it gives a better indication of how much the flight actually is.