You just sketch out what you think you want the layout to look like, and send it to Tim at Mianne. He feeds it into his CAD program and generates a BOM for your benchwork and a price. Here's a couple of shots of what I got back for mine. I did some changes on the fly after the fact, but here's where I started. I ended up adding length on either end and eliminating the 2nd level shelf in favor of a train yard. I also filled in part of the middle on the right. When you get your Mianne shipment, it comes with assembly instructions for the job, quite a slick operation. No sawdust until you start putting the top on...
If you have an afternoon to kill, you can see my build in excruciating detail here!