This is a very complex topic, but it would be good to start with this post on our forum by someone who has built multiple guitar rigs:

In general, it's very important to make sure you know what you want to have on your pedalboard, and test everything first to make sure you like the pedals you've chosen, and that the pedals sound good together in the order you've chosen. Adjust your pedal choices and pedal order as necessary. Once you've got it set up the way you like it, you can start to lay out the board as mentioned in the post.