I use a similar filler, but with two valves at the top instead of a 3-way.
Here's what I do:
1. Adjust filler stopper height to be 1/2" above bottom of bottle.
2. Sanitize bottles, caps, filler, and lines.
3. Chill bottles w/ caps placed on top.
4. Close all filler valves.
5. Using a "T" on regulator output, connect CO2 to filler and keg (keg and bottle are kept at exactly the same pressure this way).
6. Pressurize keg to 10PSI.
7. Connect keg out post to filler.
1. Press filler firmly in bottle, then open top valve to CO2 position, pressurizing the bottle, then open lower valve for a few seconds to purge air out of bottle.
2. Close the lower valve, then the top valve.
2. Turn top valve to "keg" position, no beer should flow yet. Then slowly open lower valve to regulate flow as bottle fills. Filling too fast results in foam.
3. Shut off both valves when bottle is filled to within 1/2" of top, then remove filler.
4. Cap immediately.
Keep filler firmly held until bottle is filled.
Chilling everything will reduce foaming.
Filling slowly will reduce foaming.
Higher pressures (up to 15PSI) will reduce foaming.
Working in a shallow basin will contain the inevitable mess.
Once you have filled a dozen bottles this goes very quickly, but there is a bit of a learning curve.