Once wort is cooled and you are ready to transfer into the primary it is a REALLY good idea to strain to the wort to separate the hops out. Historically I have done this by carefully pouring the contents of the kettle through the funnel trying to leave as many hops in the bottom of the kettle as I can.
If you strain the wort the resulting ale will have greater clarity and reduction in bitterness caused from the wort sitting on the now spent hops. I use a regular kitchen strainer locked into a funnel. There are also purpose built strainers and screens for those who enjoy convenience. Alternatively you can place hops inside a purpose built container during the boil.