Setup wizard allow an easy board configuration, you just need to follow steps.
It can be accessed from the Welcome tab (the big yellow button) or from the Tools menu > Vehicle Setup Wizard...
"Time out while booting. You will have to manually upgrade the board using the uploader plugin"
Most CC3D boards still use the old bootloader (v3), you may need to update it to the bootloader v4 and got working the automatic reboot needed for Vehicle Wizard.
See how to update the bootloader here: Firmware Tab
Take a look at the following pages: