Just to add a little to what that very good article says: start by setting the idle control algorithm to "PWM warmup", then go into the "Idle PWM duty table" and put numbers in there that get the idle speed close to correct as the engine warms up. Use this opportunity also to make sure your PWM idle settings (valve mode, port, 3-wire mode, and frequency) are correct.
Then... don't do anything further with the idle valve control, instead focus on getting your fuel and ignition right in the idle area. You can go in and fool with the PWM idle values to raise and lower the idle speed to make sure your timing/fuel settings work well.
After you've done that, then you can start getting closed-loop idle working. Reset the algorithm to "PWM closed-loop". On the closed-loop idle settings screen, set the open and closed duty to the numbers you mention above, "Min duty for PID" same as the closed duty, and "RPM with valve open/closed" to the engine speeds you see with the valve open and closed (if the engine stalls with the valve closed, just enter a low number like 400).
Leave the other settings at their defaults except set the target RPM table to the idle speed you want over temperature. Set proportional and derivative gain to zero, and integral to a low number like 20. Also at this point if your default dash in TunerStudio doesn't have a gauge for "Idle PWM%" I'd strongly suggest adding one so you can see what the idle valve is doing.
Then start the engine and start tuning the integral and proportional gain (leave derivative at 0 for now). Raising "P" will generally make the engine hit the idle speed target faster, but can cause it to "hunt" (overcorrect). The "I" term works similarly and increasing it can get the speed closer to the exact number you want, but again too high a number will make the engine hunt.
There is more info on tuning and some of the other settings here: http://www.msextra.com/doc/ms3/Idle_Control.html
Keep in mind that with an aggressive cam, the idle can only get so smooth and you don't want the idle valve constantly trying to "chase" a varying idle speed that it has no hope of keeping up with. Keeping the "P" value low can help with that situation.