How do I make sure I'm removing the scratches from rougher grits when I work on the finer grits?

There is a very simple way to confirm this.

As you are about to remove your piece from the rough grit wheel, hold it in one place for a few seconds so that all the scratches from the rough grit are going in one direction.

When you grind your piece on the finer grit, start off by grinding in the same direction as the scratches created by the rough grit. As you are grinding your piece, move it a quarter turn, effectively making the rough grit scratches perpendicular to the newer scratches created by the finer grit.

You'll easily be able to "see" any rougher grit scratches left in the glass.

We've also had many customers use a permanent magic marker to draw on the surface after the rough grit grind. When they move to the finer grit and all the magic marker disappears, then they ground out the rough grit scratches.