Hey, Jamie! The Neo-D is a fairly low output pickup and requires boosting the Master Gain on TWA almost all the way up.
You'll want to drop the Master Gain level to a point that suits the hotter output from the M1. Here's a video on setting Mater Gain. https://support.tonewoodamp.com/a/solutions/articles/17000016254
I use my TWA with 2 different guitars and pickup systems. A Seagull Artist Studio with an LR-Baggs Anthem and a Taylor GS-Mini with an LR-Baggs M1A (active version).
Both work extremely well but need different settings. The TWA lets you save settings for more than 1 Guitar Pickup system. When you find out what works best for a particular Guitar/pickup just save it and recall it whenever you use that particular system. A magnetic system should be fairly easy to control. Basically it's just a case of trial and error. I'm sure you'll come to terms with it.
Nicolas has given you a link to the Master Gain Video. That should help. I would also advise you to check out the other informative videos available regarding the TWA.
Have fun trying out the possibilities.
Thank you for the tips, Tony!