MSEFI is a forum specifically for users of MegaSquirt. It has a lots of information about the MegaSquirt ECU.
MegaManual is the bible for the MegaSquirt ECU. It covers many details about this great ECU. If you want to understand more about it, read the manual.
MegaManual tuning section. This chapter in the MegaManual deals specifically with tuning. Note the CIS to EFI kit comes with a base configuration and VE table so the tuning is already 95% done. You may only have to do some fine tuning.
TunerStudio is the current software for tuning the MegaSquirt.