Have to say I am with dale_the_noob as I agree with all he says. My first layout, Jaxn Junction, came about through working with the parts I had in my arsenal and adjusting the plan to fit when the geometry was a bit off, this involved a bit of extra track being purchased. I then drew the layout on paper marking each of the parts so I could relay it in the future. Typically I then bought more stock and had to amend geometry here and there to incorporate space for the extra train(s). As I have not had Jaxn Junction down for a while but have been increasing my rolling stock and locomotive stock I discovered that Jaxn Junction no longer has enough room for all the extra trains. I have designed The Water Belle Line layout using Rail Modeller, but, as mentioned in the relevant thread, it is way too big to build in the space I currently have available for the layout to be temporarily down, so I designed the Train Tryout Loop which was, again, designed on Rail Modeller (and used the current stock of track pieces), but even this will be insufficient for all the trains I can run. On it's first outing there was no room for my wife's Hogwarts Express, and the Bachmann EMUs (2EPB and 4CEP) were not operational as I wasn't sure about their coupling and uncoupling. I may tinker with this one to get all the trains up and running.
I have drawn up a few plans on Rail Modeller which are still under consideration (and all fit in the current space available) but I fear that to build a decent layout will need a bigger space! Whose doesn't??
Playability is key for me as I want to have proper running and I realise that I may well need to have a massive fiddle yard to allow all the trains to be stored. I have no experience of scenic modelling but would be interested to give it a go someday.
In summary then, I think most layouts have to have a starting point in your head and the track plan programs help visualise the parts needed to construct it and how the geometry will work. Pen and paper could still be useful for jotting down the basic idea but having Rail Modeller has given me a much better indication of how the parts will fit together.
All change! All change! This train terminates here.