Well, usually I use BandLab's AudioStretch function to listen to the audio more closely, at any speed or octave level I prefer. If I'm having difficulties hearing a specific part, and if the track is from a chiptune-based game, I use
foobar2000, a really handy tool for that sort of thing. Believe me, learning to transcribe by ear doesn't happen over night, but once you've practiced enough, the difference between where you started and where you ended up is night and day.
Seriously, I cannot recommend practicing transcription by ear enough. We all started at the point you're at, but it will pay off in the end, trust me.