The best way (in my opinion) is to just place the notes manually in some editor, or, if you can't due to timing/knowledge constraints, make the game read beats and convert them to seconds instead of storing and reading seconds directly. Beats are both rhythmically precise and human readable, so they work great for charting. The formula to convert a beat to its time in seconds is:
(60 / bpm) * beat, where
bpm is the beats per minute of the song, which can be found accurately using tools like
this.
For example, a note on the fourth beat in a song at 120 bpm is:
(60 / 120) * 4 = 2 seconds.
If you wanted something on a halfbeat, you'd just use the beat + 1/2, and similar for quarter beats, eighth beats, third beats, sixth beats, and so on, but chances are, the song you have there won't get any more complex than 1/2 or 1/4. Hope I helped!