I wait a little longer than most to transplant the clones into the baskets.
It is possible to transplant a clone into the basket right when you see a root pop out of the cube ... but I wait until MANY roots are coming out from the cube (sometimes, a root will even grow vertically out the top of the cube). When cloning, I use those little black rockwool trays ... each tray holds 6 cubes. These trays allow the roots a small dark and humid place to grow under the cube and direct a lot of the root growth out the bottom of the cube. I wait until the longest roots are 2-3 inches long.
The longer roots allows you to make sure that there are roots on the bottom of the basket, and that the cube is not sitting in a pool of water (which can cause stem rot). For this first fill, I cheat a little. I will fill the reservoir right to the bottom of the baskets (where I know the roots are) ... Ensuring that none of my fragile clones will die of dehydration (which happens damn fast to young clones without a water supply).
After all the clones have thier legs in the water, your water level should be, at maximum, within 1" of the bottom of your baskets. Always keep your water level above the halfway mark ...below that, the ppm soars and you plants will hurt.
Welcome to the wonderful world of hydro Elzz
You'll never look back
C.C.