ModFit is not an user friendly sw. Basically open your sample, choose what channel (parameter) you want to use for cell cycle analysis, define first on your FSC/SSC histogram population you want to analyze, second gating should be done to select single nuclei/cells (PI-H vs. PI-A). Now you should see the familiar cell cycle profile. Than select regions for G1 and G2/M and click on "analysis". (I hope I remember names of these buttons correctly). It is useful to log in as an administrator (psswd is either Omega or omega) to have access to all settings. I don't like their auto analysis modes and wizards. Good luck!
I can help you with using FlowJo to analyze your dataset, let me know what particular questions you might or email us at [email protected] for more help.