To import your F.E. chart in progress, you'd need to convert the chart to MIDI format (use the "Freetar Hero SNG to Frets on Fire MID converter" function at this website):
http://www.nukular.ch/foftoolsEOF can then import that MIDI (File>MIDI Import, browse to the converted chart file and click Open). You can place notes during playback, but you'll need to change the "input method" in File>Preferences to either "Guitar Tap" or "Guitar Strum". The former places notes when you press fret buttons (allowing you to place individual notes), the latter only places notes when you press a strum key (allowing you to place chords or individual notes). By default, F1 through F5 are used for frets 1 through 5 and Enter and Backslash serve as the strum buttons. You can connect a Rock Band/Guitar Hero controller before you start EOF, and as long as your computer recognizes it, you can tell EOF to use the controller's buttons to place notes by going to File>Controllers, clicking Guitar, selecting each item, clicking Redefine and then pressing the desired button on the controller. Then when the menus are closed out, you can start playback by pressing Spacebar (or clicking the green play icon near the top right of EOF's program window) and then adding notes while the song is playing. This is the bare minimum to get started though, there are other things you may want to consider such as increasing your audio buffer size (File>Settings) if the song lags/stutters during playback and grid snap (so notes are moved to partial beat intervals, such as every half a beat instead, which will help with timing issues that will come up when charting a song "live"). The Help>Keys menu item will give you some basic shortcuts, but it's also worth reading the included tutorial (Help>Tutorial) for an introduction to creating a chart. If you want to know what any of the menu functions do, they should all be documented in the manual (Help>Manual).
Let me know if you have any specific questions.