Whenever you have a piece of glass that you can see through you MUST wash off any markings that go to the edge of the glass before you wrap that piece in foil. This pertains to clear colored glass as well. Look at the picture below and notice how the black marker runs off the edge of the glass. If you wash the glass after it's been foiled you will still be able to see marks on the glass.
Below we have a perfect example. From the back side you can easily see the marker that was covered by the foil even after the rest of the numbers were washed away. Since it's under the foil the only way to fix the problem now is to remove the foil, wash away the marker, and re-foil it. If you don't notice until after the window has been soldered you only have two choices: 1) break out the piece and replace it, or 2) live with it.
An ounce of prevention is worth a pound of cure. Doing it correctly from the start, no matter how pressed for time you may be, will always save you time (and effort) later on down the line.
Bayou Salé GlassWorks