I currently have 1 2 and 3 on. I don't know what the HHKB layout is as well as the lite ext.
Note: I have an HHKB Pro, not a Pro 2. I believe the dip switches are identical, but I could be mistaken.I have 2, 3, and 6 turned on.
Dip switches 1 & 2 control what "extension" keys you get when pressing Fn. Scroll down to the 'Happy Hacking Professional' section of
this page for diagrams.
1 off + 2 on is Macintosh mode; it basically enables all the Fn-key combinations.
However, in the instruction sheet, there's a note "*1 SW3 is disabling in case of Macintosh mode.", so in my case, it probably doesn't matter that I have switch 3 turned on.
Switch 6 seems to work for me. Pressing a key wakes my MacBook Pro out of sleep mode just fine.
I don't remember if I've had the USB cable plugged in while making DIP switch changes, but my assumption was always that the keyboard would need to be unplugged/replugged for it to re-read the DIP switches.