Well if the song has its own track then you can just right click on the song in iTunes, go to Get Info, Select the Options tab and then change what time you want the track to start.
If it's the same track as the last song the way you could get around it without an editor is to copy that song so you have two of them listed and do the same thing as above. That way on the second copy of the track it would skip the main song and go right to the hidden track.
The last thing you could do is import the CD as an MP3 rather than M4A and then use the program you are talking about.
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