I have a few different methods of working but one key thing is to always start out with a sketch- if you go straight into it with pixels it's hard to gauge your anatomy because you're so zoomed in and thing's won't look right. From there on it's really just a matter of lining and colouring. Knowing how to place your shading and line neatly comes with time. You can always do your shading on a separate multiply layer though as that's much easier and quicker (Though it's a bit cheaty/not the proper way of pixeling). A great tip as well is to keep on flipping your canvas to check it every once in a while - and this goes for all your digital art, not just pixels. When you flip it, your brain thinks it's a new image and so sees it with a fresh view, meaning that all the odd looking bits your eyes had become accustomed to suddenly pop out at you - and you can fix them!
I don't know what program you are currently using, but if you need more software-specific help or advice, let me know! Hope that helps!