while general layout is up to you, may i make a suggestion replacing the second turnout on your upper yard from left for a right hand one (diverging track to midle line , straight to the last). you will have proper ladder this way.
Rail Moddler is the track plan software, im on a mac so this one is compatible there are alot of windows based ones on the market.
i used google sketch up to do the 3-d rendering
yea you cant save or print
Do you know what each of those tracks will be used for? You have five crossovers, and some, like the bottom one, leads to another long stub track. You can only enter from one direction and you'll have to back your train back out of the stub track and all the way around the curve to get the train back to a main line. The stub track on the left hand side of the layout leaves you in the same situation. I suggest you look at those side tracks and see if you really know what purpose they serve.
