Honestly the soil just keep the rockwool plug in place, they do have trays that hold the smallest rockwool cubes but I use soil and when the clones root I just grow em in there for a few weeks while the root zone builds. You should be able to use the hydroton in cups. The plugs are pretty cheap though its like 100 for $13-$14
http://htgsupply.com/viewproduct.asp?productID=51270
Can just stick that into the hydroton. You can also use those cubes in your cloners w/o the hydroton.
Heres the cloning tray that holds the small cubes
http://htgsupply.com/viewproduct.asp?productID=51361
(thats prob better for your setup, after they root just take out of the tray and put into your hydroton. I know ya got money invested into the cloner, this is just another way in case you dont like the cloner