RDWC setup questions

Hey all,

I'm going to be converting my DWC into a RDWC soon and I have a question about the setup. It seems to me that if the drain pipe is at the bottom of the buckets then the roots would grow into it eventually plugging the system. My thought on how to avoid this is to place the in line at the bottom and the drain at the top so that it drains like the overfill on your tub. How are others handling this, or is it a non-issue?

I used 3'' pvc pipe to connect each 13 gallon site. Still never liked that system as much as the Ebb and Flow.