Nios II won't work after uploaded to the board

clock definitions and timing constraints are written in .sdc files when you use Timequest as a timing analyser. Have a look at the reference design and look for one or several .sdc files. Hopefully it will contain all the timing definitions that you need for your board. Copy the files in your project folder, add them to your project and recompile. Look for critical warnings such as "timing requirements not met". If you have those then you have a timing problem.