I have a aeroponic setup all ready to go, but i am going to be starting from seed(Dr GreenThumb's Endless Sky). So The question is whether or not I can go directly from seed in the aero unit, and seperate the males without worrying about hurting the other plants roots? I ask this because I remember reading something about this being a problem, but it seems like if I flowered them when they were only twelve inches like the site says the root mass would be small enough to avoid this problem.

Any opinions are greatly appreciated

No, root grow like weeks. No matter what they will get tangled. You can risk it. If everything else is okay with the clones you can beat up alot of roots with out killing the plants.

ok thanks for the imput, so do you think pulling the roots apart after say 4 weeks of growth would be enough to kill the remaining plants or not?

nope. 4 days no problem... 4 weeks problem.