disclaimer: i dont have an mspfa of my own released (yet) but ive been doing some research on some of these things for my own practice, so take this with a grain of salt ahaha

afaik lots of people just use a standard drawing program with a pixel brush to achieve the art style. ive heard that many use photoshop but clip studio is just as good. for still panels and simple gifs, what program you use hardly matters since you only rly need a standard pixel brush, but i cant say anything for actual flashes/animations since im not really sure how to do those yet either

for more technical things you can also check out this portion of the homestuck resource site, its got stuff that may be helpful like editing tutorials and such: https://homestuck.net/resources/other.html