I use SAI when i have a ton of inspiration, if not i use mypaint.. They both turn out nice. ^^
MyPaint is free though ^^ But i'd still reccomend both of them..
Also, i'd try to stay away from pony creator.. .
When i have a large project with a ton of stuff in it with most likely a group of ponies i like to sketch it out on paper until i have a picture that i like and then i sketch out the final picture i chose digitally, Then you've gotta do lineart.. base-colouring...Shading, background colour, and then if im really pleased with it i get exited and run it through some photoshop filters to