No need to worry about the order you do things in. There are exceptions when it comes to patches, hacks, etc., but bringing them up now will probably only serve to confuse you. How full or empty your drive is doesnt influence these things anyway.
For now just install what you'd like and deal with those "hiccups" when/if you get to them
Things like skinning, new icons, etc. are tiny (a few megabytes), so there'll be no problems.
