Chris, I've found it useful to write down my goals for the layout. If you take a look at the first page of the PRR Panhandle 2.0 thread (in the Photo sub-forum) you'll see what I mean. At some point, you need to start construction, but adequate pre-planning is extremely important.
BTW, I found under-the-layout storage facilities to be a total PITA. Of course, your mileage may vary. You do have a lot of room for one.
Good luck and keep us informed.
George