I used two methods to come up with my panel layout. For the first step I used PanelPlanner J. PanelPlanner was easy to use and it allowed me to try out several different concepts with very little effort. I mainly used it to try to find the general layout I liked the most. I played around with different avionics, symmetrical/non-symmetrical layouts, etc. Once I finally decided on the general layout, I moved on to the more detailed layout (i.e., step 2).
For the second phase I modeled the instrument panel in SolidWorks. I do this for a living so it wasn't much of a learning curve for me. There are several other lower cost CAD packages out there that will do essentially the same thing. The biggest advantage I found to modeling the panel in 3D was you find all sorts of interferences you don't find when you're drawing things out in 2D. You can also see maintenance access issues early in the design phase. You've find these issues when you go to put your panel together in real life. Unfortunately the fix is usually buying more material to make another panel.
I then printed the design out full scale and taped it to the blank panel to see how the layout actually worked out (can I easily reach the switches, are the avionics in my field of view, etc.). Remember that the avionics will protrude some from the surface so take that into account when you're doing your labeling. If you model the avionics accurately in 3D, you can see this effect on the computer by rotating the panel around.
Another benefit of modeling the panel in CAD (or PanelPlanner) is you can have the panel CNC cut. I used Up North Aviation to cut my panel and I couldn't be happier. Bill did a great job on my panel. I probably could have cut it out by hand but based on how long it took me to cut some test pieces I did, I paid about $2/hr to have Up North CNC cut the panel. They have great prices and unbelievably fast turnaround. Worth every penny if you ask me.
The best thing to remember is if you screw things up, you can always make another panel and try again. You're not working with a priceless Rembrandt here. There's nothing that time and money can't fix...
I hope this helps.
Jeff