Use options to slow the rate down to 0.5x (So you can hear the beats more distinctly)
Place the first note, then adjust the Offset until that note appears when you want it to
Next, place 40-50 more 4th notes in a row, and tweak the BPM such that they are all at the right timing (Take note of if the notes are faster than the song, or song faster than the notes, then change the BPM to make it closer).
When you're really close, use Sync Song Tempo (Stepmania V4.0), and it can do the fine tuning for you. Else, just work with the BPM until it's pretty much perfect.
The farther you go, the more accurate you need to be. What may seem sync'd 1 minute in, may be half a beat off a minute or two later. Just takes another small tweak.
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