When abusing for your ID/SID, you should put in the delay you're wanting to hit. You hit A right before you shrink at the end of the second timer, check what ID you got. See what delay you hit, and adjust the "wanted delay" higher or lower depending on what delay you hit.
For instance, if you were wanting a delay of 4,000. I would put 488, 4000, 15, 15 (calibrated delay, wanted delay, calibrated second, wanted second). I would hit A at the last message Oak says, check the ID I got, input all the correct data into Pandora's Box (you'll see the delay checker on the far right), and than if I got a delay above 4,000. I would decrease the wanted delay by a few, and try again. If I hit a delay that is lower than 4,000. I would increase the wanted delay by a few.
I wasn't saying start a thread, there is already a thread for anything that is not 5th gen abuse.
You ask all 3rd and 4th gen abuse questions in the Most Generation PRNG Help / Information which is found here: http://www.smogon.com/forums/showthread.php?t=52180
The first one is more of what you're going to need to read, the second is useless and is mainly meant for Honey Tree abuse which is solely used in DPPt.
When using the calibrated delay, that means whatever your fastest delay is getting in. When HGSS abusing, I would always leave the calibrated delay at 488. Never changing or altering. No matter what type of abuse I was doing.