Converting unprotected M4A files to MP3 should work fine in MC, so long as you can play the M4A files back correctly. However, please note that you CANNOT be using Quicktime as the playback engine. You need to be using DirectShow to play the M4A files. You can tell easily which is active if your visualizers work when you're playing the files back in MC (no Visualizers mean Quicktime's engine is active).
The easiest way to solve this, if you have the issue, is to
install CCCP.
You set the supported file types for your handheld in the handheld sync options, under Tools -> Options -> Handheld. Select your handheld from the top drop-down, and then go under Files, Paths, & More and change the Supported Types from "*" to the extensions you need. It is a semi-colon delimited list. So something like this would work well for an iPod:
mp3;mp4;m4a;m4v;m4b;m4r;m4p;jpg
The HiFiMAN supports FLAC and other formats though, so you'd want to use your own list.