You'll prevent a lot of possible problems if you take your clones at about 4 inches tall. Your rooting solution should be a mix of rooting hormone and an antibacterial mixed into your water. Get a small light proof container full of the rooting solution ready for each clone and then cut the clones. Immediately after cutting them, hold them under water in a nice large container and cut them at a 45 degree angle while under water. This will eliminate any air bubbles from blocking the veins of the stem. Then put the cuttings directly into the small rooting containers and place them under a moderate light for 24 hours. The clones will first wilt and look like hell, but by the next morning, they will be standing tall.
The next morning, start moving your light closer until it's at it's maximum lumen height for the type of light you're using. Only move it about 3 inches closer each day. The cuttings will love it. Don't get the light too close and burn the cuttings.
Make sure you keep the rooting solution fresh. Change it each 5 days.
After about 10-14 days, you should see roots developing on the stems, below the solution level. Let the roots develop until they're about an inch long and then carefully transplant the cuttings into whatever growing medium you're using.
Good luck man!
