You will have a couple of moments with clip-ins - usually when an instinctive reaction is required and you haven't quite developed the instinct. But this will soon develop.
The advantage of these is that they offer more flexibilty as to what muscles you use.
A basic example is that you can use them to turn a wheel when cruising(this entails applying pressure to the crank throughout the 360 turn by pushing down,pulling back,pulling up and pushing forward all in one movement). This rests the muscles used for say, pressing down on the pedals for when you want to accelerate or climb a hill.
This all takes a bit of practice - so keep at it!