The easiest way to set the encode clock frequency is to tune to the exact frequency of an accurate signal (WWV on 10 MHz can often be heard in the UK) and set a narrow filter width, DSB mode and tuning step of a little less than the filter width. Make sure that the QS1R Verb has been running long enough to reach a stable temperature and that there is a reasonably good signal level from the accurate source. It's easier to tell the difference between high frequency tones than low ones, but the wider the filter is set, the more noise is heard.
I used the 500 Hz filter width and dragged its edges a little wider with a right mouse button click and drag. Then, with the tuning step set to 500 Hz, I rocked the mouse wheel one click above the 10 MHz position and one click below it. When the encode clock frequency is accurately set you will hear exactly the same tone at 10.0005 MHz as you do at 9.9995 MHz. So it's simply a matter of changing the value in the text entry box until the tones heard at either side are the same. The number needs to be reduced if the tone at the upper side is higher than at the lower side. I ended up with the value 124.99638 and feel reasonably confident that it's as accurate as I can get it.