your not going about making your tree in a very painterly way, your thinking about it too much like doing a drawing, when in fact pixels behave a lot more like paint than pencil.
stop doing outlines, stop using the pencil tool, and stop copy pasting stuff all over other stuff.
take a small brush, get 3 colours, one green and one brown, and one colour of your choice for the background, and draw a brown stick, then blobs of green. repeat until u get something that has the form of a tree u like, save. then take a pencil tool, select one of the colours and add/ subtract to the blobs, the trunk/branches to make them less blobby at that small one pixel scale, work like this until u get a result your happy with, save again. post your picture as of then here, and well critique you on how it looks what you should change ect, and finally you can begin shading. YOU NEVER DRAW ON OUTLINE FOR ANYTHING, EVER for this exercise at least.