how do u build a edd and flow the cheap way

[hatecable]

I use one of these. 11 Plant System with great success. cost me about $15 minus the soda bottles.:rasta:

I looked at that system and looks pretty cool and fun to make, but how do you keep the roots from plugging up the 1/2" hole in the caps? I wouldnt think it would take long for it to become a problem. Cut the roots?