Its fine to touch the mobo tray as long as its not metal (acrylic, wood etc).
Drill some holes around the case for ventilation if it has any performance parts.
I will post some of my custom cases to give you ideas if you want
The mobo must absolutely 100% NOT touch the case if it is metal. You must use the riser screws gamerz posted.
Lining up the standoffs for the mobo is a pain in the a** - I went through about 20 before I got it perfect