http://mainsequencesoftware.com/Content/SGPHelp/SequenceGeneratorPro.html?UsingEQMODwithSGPro.html
Did you follow this checklist? Are you using an EQDIR module? I tried helping someone with EQMOD and the end result was it doesn't work correctly unless you have the EQDIR module.
Meridian flips are something you can practice during the day. Just turn off guiding/centering, slew to a star near the meridian and command meridian flips manually using the button the 'telescope' tab.