The best results would involve using a MIDI editor like Anvil Studio (don't use Fruity Loops, it won't do the job), and rename the text events that contain things such as "section
somethinghere" and save the MIDI (make sure to keep a copy of the original). You can also do the same thing in EOF, and it will be more convenient since it will allow you to play the audio to hear what part of the song each section marker is at, but the MIDI timings will be rewritten when you edit and save the chart in EOF (all note are rounded to the nearest millisecond during import). The loss in timing is negligible, but it's worth mentioning.
More details about section markers is here:
viewtopic.php?t=7236