Qsys 13.1 tutorial

Try the Quartus II handbook:

https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/hb/qts/archives/quartusii_handbook_archive_131.pdf

It has several chapters on QSYS.

Basically QSYS has a library of components already in it, so. Since you are using a custom CPU, instead of NIOS, it may be a bit more complicated, but you should be able to expose the avalon bus and make a wrapper for your CPU to talk to it.

Pete