Mark,
I don't know your type of densitometer, but I assume its for measuring density on film.
In that case, you have to measure a density at the leading end that has no information in it. It should be blank, but normally developed and fixed. When you measure that spot, zero it on that. This means that the densitometer from now on displays the density of spots and excludes de negative-base and fog. All measurements wil be offset by the spot you used during the zeroing. In other words: all measurements are subtracted with de density at the zeroing spot.
Normally density wil be denser than the zeroing spot, and therefore display a positive value. If you see negative values, your last spot is less dense as your zeroing spot!
I hope my English is good enough for you to understand what I mean....I live in the upper part of Holland, called Friesland.