Determine the basic song structure. Find out what order the sections (verse, chorus, intro, etc.) go in and how many musical bars are in each. Define these sections for the full song out on the sheet music of the transcription.
Transcribe the percussion track. Isolating out the lower EQ sections can be helpful. Having this section done first gives a skeleton to the transcription and is helpful for getting the note durations in other sections.
Transcribe another instrument, but be sure to choose one to focus on at a time. Adjusting the EQ and balance on the player can help to isolate that instrument. Since each instrument has its own pitch range and balance on the recording, these settings need to be played with.
Transcribe each instrument one at a time until the score is completed. Usually it is a good idea to go from simple to more complex, but this varies based on the song and transcriber.
Test the score out against the track to make sure there are no discrepancies. Alternatively, the sheet music can be programmed into a MIDI program and played to see if it sounds correct.
Adapt the major parts of the song to a desired instrument or ensemble if making an adaptation. Depending on the nature of the adaptation, the parts used in the transcription can vary. The main melody and basic bass line will almost always be used.