mux warning "Clock multiplexers are found and protected"

As a general tip, if you want more information on a warning or error in Quartus, just right click on the error or warning and click help.

I don't hink you need to do anything unless you have a reason to. Quartus is just telling you that it did in fact recognize your multiplexer.

Read the HDL coding guidelines for multi-plexers beginning on page 6-61 of this document:

http://www.altera.com/literature/hb/qts/qts_qii51007.pdf

Jake