"SoundCheck is really more trouble that it's worth. I'd suggest using MP3Gain to both calculate the ReplayGain tag and apply the gain to the MP3 file and not use SoundCheck at all.
Here's why using SoundCheck is such a pain:
By default iTunes scans each track for loudness information on a per-track basis. You probably want your songs scanned on a per-album basis. So you have to use another program to scan your library. iTunes doesn't use the ReplayGain tag information, it does its own scanning. However it does cache the scanning results in the COMMENT ITUNENORM tag field (in an iTunes-specific binary format). So you have to use another program to write the COMMENT ITUNENORM tag field. In iPhone OS 3.0.1 (on my 3GS) SoundCheck isn't applied when listening over bluetooth headphones. (I don't know if Apple did this on purpose or not.)
The last two bullets are what finally drove me away from using SoundCheck. If you want to use the ReplayGain information, you have to convert it into the iTunes SoundCheck format (before you add the song to your iTunes library). There isn't very good software to easily do this conversion. Mp3tag will do it (here's how) but it's hardcoded to use ReplayGain's default volume of -89dB, which is too quiet for my taste.
I've been much happier just applying the gain directly with MP3Gain."