If you are running a flood/drain system you should not be flooding the rockwool at all. Flood to about 1/2 inch below the cubes.
Once you have your system setup this way you can water from 3 to 6 times per lights on. The reason to water so many times is that the hydroton wont hold much water and as an added bonus every time the tray drains it brings fresh air to the roots.
The length of time it takes to fill your tray to the overflow is the length of time you should flood for (generally 2-6min).
Hope this helps - good luck!!