If there is only a few roots growing strait down pack your pots you are moving them into. Water them down(water temp room temp or slightly warmer) and add more soil if you want then water again(great time to check and adjust pH). Let them drain for about 10 minutes. Poke a hole in the soil with a pencil or something as big as needed for the roots to not touch the soil on the way down(prevents damaging the roots). Once the clone is at the level you want hold it very still while you push the dirt around the stem in and down a little to hold the plant up and support it without compacting the soil too much or breaking the roots, but enought so that it can stand up pretty good. The soil isn't right up to the roots so be careful. In a few days the roots will reach the soil and a few days later it should be pretty stable if you haven't damaged any thing.

If you have a knot of roots starting then you kinda have to do the same thing but dig a hold and gently dump moist soil in around it's roots, but keep the plant and roots very still til you compact the soil again by the stem to support it.

Be careful and gentle and your plants will reward you, be sloppy or slip and your plants will forgive you but it will take as much time as the damage done. At this point you can sigh with relief because the survival rate greatly improves and it's time to grow quality plants instead of just keeping them alive.

Good luck.