Timers perhaps?

[skimask]

With this code, Pin A.6/Clkout is putting out a 1Mhz stream. With the selected prescale, the interrupt will fire on every 4096 ticks of the main clock. When the interrupt fires, it sets port B.7 high, then low. Effectively, this gives me a 1Mhz signal on A.6, and a 244Hz signal on B.7. I'm not trying to generate the "fast" signal, as that's done by Clkout. I'm just trying to generate the "slow" signal.

Aha! You see, the problem is, you didn't tell me that you were going to use ClkOut for one of your pulse sources!
Now this makes sense...
Yes, this should work exactly as you describe.