Try using a program more suited to an easy pixel work flow, like GraphicsGale, Pixen (mac), Pro Motion, or even just MS Paint. That program you're using seems to break everything into tiles and has no real 'canvas'. Not to mention an apparent lack of any sort of palette tools? This breaks up the work flow and distracts you from what you want to focus on... the art.
I also suggest finding some reading material on classic art and drawing. Learn how to see objects as 3D forms that are communicated by sections of light and shadow. Trees can actually be a very tricky subject. I recommend do some reading on drawing (study), and do a bunch of sketches with pencil of trees, focusing on the techniques you've read (practice). Once you've got a better understanding, you should be able to translate the concepts into pixels.
Really, starting off a pixel art piece is no real difference to any other material or medium. You decide your subject, basic palette, composition, then block in the major sections of light and shadow, then refine iteratively until you're satisfied the piece has reached its potential. I'm sure everyone has slightly different work flows, so asking what is the best way to start will give you a whole bunch of different answers.
I guess I've given you mine