I wasn't exactly asking how to use the software, I am pretty decent with software in general, just lacking experience on how to proceed.
The thing you said about hand drawing before confused me.
My bad, my process usually is,
-I will look at other people's pixel art for reference.
-Once I have an idea of what to go for draw it with a pencil on graphing paper (1x1 square block paper used in schools for Architecture graphs/tables and geometric patterns) You can probably get it at a bigger grocery outlet, if not an Office Supply store for sure.
-Then put that above my keyboard then zoom way in on Greenfish and just re-draw what I have on paper. I separate the parts I want to animate into layers, and just copy the object along a sprite sheet and then make the variations.
But again, we are all Game Developers, I'd check out
http://pixeljoint.com/forum/
https://www.reddit.com/r/PixelArt
http://pixel-artists.deviantart.com/