Identifying the right motherboard for a project
If you are talking about a computer motherboard, I just use the Newegg power search. As for designing a single motherboard, thousands of man hours go into designing just one. And even some of the simplest still have many more than your typical 2 sided layout. There is also no "motherboard templates" that you can customize. 

If you are talking about a interface board to link your many components together, you should start your design with the correct headers for your "daughter boards", and then add the processing power as needed. As for templates, I don't know of any off of the top of my head, but if you use header pins, you shouldn't need a template.