I usually like you say, just have a noise at the start, record each track separately, then zoom in and line up the waveforms. Never had any issues at all with the tracks not being perfectly in sync.
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I just use an aux cord and audacity. Use the amplify feature for leveling. Also make sure you don't record with the volume all the way up, as the amplify effect will fix the volume. Like that raw sound. :^)
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Thank you guys for sharing! I've used both methods and I also love that raw chiptune feel 
I'm just interested in knowing more 'thorough' ways of recording those lovely DMG, GBA, GBC, DSLite etc. 
Changing the approach a bit to get different results...
There's nothing wrong with just recording directly even from the headphonejack, but summer is coming and I'm gonna have more time to try out new fun set-ups to produce great new lo-fi/chiptune music