Peeps generally learn in 2 ways ....
1. Meticulous planning - carefully measuring each component and case dimensions, making component markups out of cardboard, making CAD drawings, etc.
2. Trial and error - essentially doing it wrong and then learning what not to do the next time
As for what tools....
Color - paint spray can
Round holes - drill
Irregular holes - dremel
This guy is an idiot but I like his tool set
http://www.overclock.net/t/1434002/wc-tools-thread