I have an EWI as well, but don't get to use it very often. I'm about in the same situation as you. Here's another EWI-related question that you might find interesting: What is needed for an electric woodwind?. Some of my answer here may overlap with things I said there.
I briefly tried the flute fingering a while back, but I generally keep it on the recorder setting. Partly because I'm more familiar with recorders than flutes, but also because the recorder fingering seems to have a larger overlap between octaves, which gives me more fingering options.
In my experience, I'd say the key thing to keep in mind while practicing, is that an EWI is not the same as the acoustic instrument its simulating. While there are many similarities, the EWI will generally be less forgiving of sloppy fingerings than the equivalent acoustic instrument. This involves a bit of humility, because at first, you feel like you should be able to use it pretty easily, but then you find out that it's different than you're used to. The tricky part for me is getting all fingers to move at precisely the same time, without getting a quick "blip" of a note in between. Sometimes I'll just break it down to a single pair of notes, and slowly practice getting the transition as crisp and perfect as possible between those two notes. This especially true if there's a register shift, involving the thumb-roller.
When programming the DAW (I use Reaper), I generally turn off the velocity response (i.e. map all the incoming notes to a fixed output velocity). Instead, you want the volume to come completely from the breath control, which will give you better, more consistent, control of volume. For example, this will allow you to start a note softly, but still be able to swell the note to a fuller volume. If you used the velocity, and started softly, it would place a cap on how loud you can get the note later.
One really important thing that I've discovered is that there's a different breathing technique. The EWI doesn't allow all the air to pass through the instrument. It's based on static air pressure, not velocity. As a result, after playing a full phrase, you might find yourself needing a breath, but your lungs are still full! This means you have to exhale before you can inhale. The trick here is to "leak" air from the corner of your mouth (this is not good practice on most wind instruments). With a bit practice, you can control the air leak rate to both provide proper dynamics, and end-up with empty lungs by the time you're ready to breathe again.