I've never used miniatures in game so I would like to know to try to make something useful. :)
I'd recommend to draw them so that when you print them they are 1,5-1,8 inch tall. This way they are in proportion with most existing miniature. You can make them bigger and scale them down to the right size as well.
I'd recommend using existing paper miniature as a height reference. I have a free miniature packet if it can be of any use.