I'll try to give you some pointers, but I haven't figured out any of these track planning programs yet.
First off you got some real good advice in your original post in the 2 rail forum, get the area ready as far as insulating and putting up whatever you want on the walls, floor, and ceiling, trust me I didn't, and I've paid for it ever since. Spend some time in the basement with a tape measure, get a feel for what will or won't fit. A friend of mine laid his track right thru his stairs, had it right up along the wall and boxed in, so clumsy person (me), couldn't damage it. Go to Lowes, Home Depot, and get some of the rosin paper, comes in a roll and with some tape and a pair of scissors you can make a template of your bench work. get some large sheets of graph paper and sketch out some ideas with features you want, yards, sidings, industries, you get the idea.
Set some standards for yourself, as far as say minimum radius curve you will accept, layout height, heck even down to what you'll build the layout out of. Remember you'll probably have to fudge on the standards a little, so be flexible, if you can't have A, well I guess settle for B. You have a nice dimensioned drawing of the basement, look at layouts in magazines and start sketching, post some of your ideas on this forum and ask for feedback, I'm new here but Ive been lurking for a while, and from what I've seen the folks on this forum, will help you out.
Look to model magazines for some inspiration, I'm looking at December 2013 issue of Model Railroader magazine, and Lance Mindheim's , layout, it's more along the lines of what I'm looking for, more switching then mainline running, scenery, locale, is up to you.