Reduced starters

[plloyd1010]

Some scenarios have units (on either side) that begin "reduced" (I will assume that means 'with one step gone'.)

Yes, that's correct. Unless the SSR's say otherwise, or you don't have a major, they are eligible for consolidation with the optional rule.
 

If those reduced units are further reduced during the game and thrown into the "dead pile" (for later accounting), are they only counted for the actual step lost in combat, or are they counted as two steps lost? If only the actual step lost in combat, how does one keep track of which is which?

They are only one step for loses, still normally double if is a reduced tank. In Vassal, I normally put units back to their original state when sending them to the graveyard (serves as a backup). There is a step loss counter on the turn track (my primary record). Of course Drew's tree-killer method always works.