What if we wanted to generate two or more high res areas inside a single level 9 tile with Helper
With the helper app it is not possible, since you can define only three areas and these only for different levels. I don't know whether the GeoConvert Tool supports more than one entry per level, but you could try it by editing the file "gch.tmc" and adding the entries manually before pressing "Start".
Am I supposed to turn off the snap when I first enter the base number and then turn snap on?
I never tried to enter coordinates manually for the large area, since these fields are normally filled by the program automatically. But you're right, manually entering values only works when snapping is disabled.