Having the two knurls not exactly in line is a function of the holder and you might be able to tune things a bit with washer/spacer or a bit of machining.
The reason that you could not move the saddle was the fact that you had the full pressure on the knurls.
What you did was correct. Turned by hand and got both knurls tracking.
Once they are tracking correctly then you can back off the pressure and then traverse the saddle to lengthen the knurl. You have to loosen things a bit as the
knurls are embedded and to move them requires allot of horse power.