I usually start with one of my template IT files (which use samples that output the exact pitch the NES will output... well, within precision and resampling limitations and some other quirks not being there). I sometimes have a tendency to not think about volume and pitch envelopes outright, except for most commonly the triangle kick, mainly because I end up programming them using the built-in Impulse Tracker effects (and typing them in the message editor for instruments manually can be tedious... plus we have the line break problem that cuts off especially long cases, when I can correct by hacking the .it file with a hex editor). There are exceptions, though, especially if I realize I have memory constraints, which will cause me to replace some of those effects with envelopes if used commonly enough. I do have to manually set up the global volume of the sample to try to reproduce the volume balances of the NES (this gets ignored during conversion).
DPCM used to be a weak point for me not because of the conversion results, but because I used an inaccurate enough player that I overestimated the volume capabilities of the DPCM. The pitch envelope feature for the DPCM (limited though it may be due to hardware limitations) allows me to make cheap, powerful kicks with a sample that's a mere 17 bytes.
I do look up the manual mainly for the pitch information on noise and DPCM.
The biggest gotcha? You have to align your instruments and MML instruments together manually . I have to be conscious about this part (and making sure they're in the correct channel) to avoid potentially glitching out the playback.