Hi
Given the way a digital scope works, you really want to use a single trace. Trigger on one channel and look at the other channel. It that's possible, you will get more samples on the screen.
So the easy way:
Fire it up so you can see 1 ns per division. If the edge moves 1 division in a second, the frequency is off by 1x10^-9. If you can only see 5 ns, wait 5 seconds (it's easier to time).
As long as you are looking at something in the seconds range, the scope's timebase isn't a big deal. If the timebase is off by 10 ppm, your 1ppb is really 1.00001 ppb. (There is only a small chance I got the number of zeros right, you get the idea). The timebase accuracy *does * matter if you want to know exactly how far off the GPS PPS is from a PPS out of the Rb.
Now, if you are comparing two 10 MHz outputs, the period is 100 ns. Watching them align edges as they drift is waiting for the to accumulate a relative time error of 100 ns. If it took 100 seconds to do this, you would be off by 1 ns /s or 1x10^-9. If it takes 200 seconds you would be off by 5x10^-10.
Hopefully that all makes sense.
Bob