As steve has said there are many advantages of hop pellets but also the disadvantage of removal.
I have found the best way to deal with them is to place an immersion chiller into the boiling vessel, use a stirring action in one direction only, this will help with the cooling and also concentrate hop debris and trub into the center of the cooling coil.
One cooling is complete do not disturb the coil and allow 10 minutes for everything to settle out. Tranfer into FV in your normal way whilst avoiding disturbing the trub and you should end up with fairly clear wort.
Any hop debris which does get through to the FV will be thrown up in the primary yeast head and can be skimmed off
