What sort of help do you need with, specifically?

The best way to figure out how to do these things is to open up the .txt and .png files in Flare, change things around, and see how everything connects together. Like in the .txt files there are various parameters, so change them, run the game and see what's different!

That being said, I'll try and answer your questions from what I know:

1) Size: This is something you can define yourself in the .txt files in the animations folder. Refer to the example provided in the alpha demo. You should see something like this:

render_size=96,96

render_offset=48,64

This means that in your sprite sheet, each sprite is 96 pixels apart in the x direction and 96 pixels apart in the y direction. So make sure your .png sprite sheet follows this.

Render offset is hard for me to explain, best way for me to put it is that it defines where the 'floor' point of your sprite is when it is in the game Mess around with the parameters to see what looks right.

2) how many and what angles: Render each animation frame of your 3D model 8 angles in 360 degrees, 45 degrees apart. make sure you render it from an isometric, orthographic view.

3) how render the poses and put them in a .png sheet: I'm sure there are shortcuts, but I am an idiot so I do it manually :P I render things out frame-by-frame, for 8 angles, making sure I take into account the render_size and render_offset.