I've not used these templates, but if you're speaking of the HDL templates I think you would normally create a new Qsys block and ask Qsys to use those HDL files in order to create the Qsys component.
Qsys will then look at the various interfaces in the HDL and build a component based on that. Alternatively, you can start in Qsys and define the block in the GUI (I/O, interface types) and have it generate a template that you build your functionality into.
My advice is to go through the qsys tutorials on making new components and experiment a little bit; for me the flow can be quirky but I generally understand how it works well enough that I don't get stumped too often. The tutorials are pretty good.
Lance