It depends largely on what your clones look like.
You are going into hydroton, so I think it is safe to assume you cloned into RW or RRs, or in a bubble/aero cloner.

Okay here's what ya do, and let me tell ya I seriously FUCKED UP my most recent hydroton grow putting the clones in! So I did what I should have done all along and asked the helpful grow-shop keeper, lol...

He told me this:
Get a nice big pot- even a spaghetti pot- that is about 4/5 full of water at room temperature. If you want to be fancy, put the pH at 6.0. Make sure that the hydroton in your system has already been treated to stabilize the pH at 6.0 as well.
Now, fill your net pot almost completely full of hydroton.
Dunk it in the spaghetti pot so that the hydroton floats freely... seriously! This is the trick!
Now, with your other hand around the RR or RW plug, somewhat protecting the roots, plunge your clone into the hydroton as it floats in the pot. Gently lift the whole net-pot out of the water, supporting the clone upright as the HT settles around the plug. You probably will have lost some pebbles, but you can add a handful to the net=pot and voila, your clones are 'seated' with minimal root damage.