Basically, assign the output in LEDBlinky (GenLEDBLinkyInputMap.exe) to something. Preferably a front end control label.
Now, in the Controls editor (LedblinkyControlsEditor.exe), in the profiles, edit the <default> profile, add the label you made for the output, and click the "always active" button in the upper right.
At least, that's how I'd approach the problem if I didn't want to hardwire the LEDs.
Honestly though, I'd just hardware it like PL1 said. Its really not that difficult. Hell, use the appropriate LED and wire it to the PWR LED on your motherboard - so it lights up with the computer is running (exactly like the PC CASE LEDs do)