Hello staskcup,
You can start with a simple setup and then build up from there. You should probably first decide what you want in your panel, i.e. buttons, switches, rotary switches, rotary encoders, leds, 7 segment displays, lcd screens. To have something to shoot for, I would suggest looking at your favorite airplane control panel and try to imitate a part of it, or a combination of things that you may wish to control. Do some sketches of how your buttons and other controls might be placed in your panel. Try to be as specific as you can recognizing the tools you may have to work with.
Your first panel could be as simple as poking holes in a cardboard box to install your controls (a shoe box would do). If you have woodworking skills, you can build a plywood box for your panel. I made my panel box from 1/2 inch plywood scraps I had and the front from a piece of acrylic. Alternatively, buy a plastic project box and use that to house your controls. You will need a drill to cut the holes for your instruments. Then you are going to need some wiring to connect everything to your mega board. I bought a connector kit, wiring set with different colored wires and a soldering iron. Those are going to be handy to make all the connections. If you have basic soldering skills, then the wiring is not going to be a problem.
A mega board has a lot of pins available (max of 68 pins), so it is unlikely that you are going to exceed its capacity, just bear in mind that Mobiflight does have some limits in how many devices it can handle of each kind: Max of 40 outputs, 68 buttons, 4 led segments, 20 encoders, 10 stepper motors, 10 servo motors, 2 lcd screens. I also recommend you draw a simple diagram of how the connections are going to be in your panel. What device goes to which pin on your mega. All of your devices will likely need a ground connection, so you should maybe plan to assemble a ground bus that takes a ground cable from your board ground pin and goes from device to device. There are also considerations to be made as to which pins you need to assign. For example, if you are going to use leds and wish to control their brightness, then you need to connect those leds to PWM capable pins on your board. Because pin 13 has a builtin led connected, it is better to use this pin for outputs only. A pinout diagram of the mega board is easy to google and will help you with deciding your pin assignments.
You will need to install Mobiflight in your PC, plug your mega board to a usb port, startup Mobiflight, which will search for your board and offer to install the firmware to convert your mega into a Mobiflight board. After that, you should be ready to start configuring your devices in the Mobiflight Modules page. See the tutorials available in this web site and on youtube on how to get Mobiflight working.
Good luck.
Jaime