So this time around I used Krita, a free open-source art program, applying some tips from this post I found. (You might find Pixilart easier to handle since it's designed for this sort of thing, as I used a similar program for the previous game.)
Basically, I started with a 96x96 pixel art, then resized it to 384x384 so it displays better. I don't remember why I chose those dimensions exactly, but that's how it goes sometimes.
Thanks! For pixel art, it can also help to do a larger digital sketch, then scale the image down to pixel-art sizes and clean it up then.
As for the images, it used to be that you could import images through the desktop app, but this appears to no longer be the case in the current version of Twine. I used this post as a guide for how I did it; it results in messy-looking code and requires a bit of a learning curve, but it works just fine on nearly any device.
It's a lot to take in, but the bottom line is this: I use this site convert the image to Base64, click "copy image", and then paste the resulting mess of letters and numbers between the quotation marks in <img src=" "> which is the HTML image tag that goes in the passage.
The alternative is using an earlier version of Twine, but I haven't touched that so I don't know how it works.
