So how to use runes when in sylph mode:
1. Do any of your regular, non sylph attacks (excluding auto strike).
2. When you see the skill words in the middle of the screen (example "Lightning Strike", "Slasher") then go ahead and awaken the sylph either with the mouse or better with the shortcut (Space).
3. The moment you see the words "AWAKEN" in the middle of the screen use any rune you want either with the mouse or shortcut ("X" or "Z").
This "Click when you see the words" method works 100% of the time!!! and special thanks to QuanChoo and Elia for sharing info about this.
Last, but not the least I also made a video on YouTube fully explaining it so you can check it out below or on my YouTube channel.