Timer0 is something you cannot control. You have to repeat the calibration process until you can determine which Timer0 value you get most often. Then use that one in your profile for searching things.
Oh to hit your seed you would just enter the DS game from the DS main menu at the specified time, while holding the required buttons. On a lite/phat you would do it 1 second before the time given in Reporter. Earlier than that for DSi/3DS.