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There are some tutorials on what you need to do on the Altera web site. Since you don't need to have it power on without loading from JTAG you can save a few steps. First of all, you can delete the on-chip memory since you don't need it to run with JTAG. When creating your system in QSYS, you should unlock all the addresses except the SDRAM which should be locked at address 0. Use the auto assign base addresses command to get the rest of the addresses set up. Change the exception and reset vectors to the SDRAM. Generate the system in QSYS and compile in Quartus. There should be no errors this time. Now you need to go to the software and re-generate the BSP and rebuild both the BSP and your application. This is needed because you've changed the base addresses in QSYS. Now you can load the software. Make sure you have reset the processor and download code checked in the debug/run configuration you use.