Live Control of PWM Outputs (need advice)

If you're not already using Qsys/SOPC Builder, then probably the easiest method is to use the In-System Sources and Probes (http://www.altera.com/literature/hb/qts/qts_qii53021.pdf). This allows you instantiate a megafunction which you connect to your control registers, and allows you to easily modify their content using a PC GUI that Altera provides.

Otherwise, you should consider adding an Avalon-MM Slave interface to your block and packaging it as a Qsys component. This would allow you to write NIOS C software to modify it if you wanted to, or it would also allow you to use the System Console (another Altera PC GUI) to read/write your register values; you can even create simple GUI's using the Dashboard functionality of that tool. An alternate approach would be to instantiate a series of GPIO blocks and connect them to the control registers of your block (instead of adding the Avalon-MM Slave port to your block).

From your description though, it sounds like In-System Sources and Probes is both less work and adequate for what you are trying to accomplish.