That seems like a reasonable thing to do, but RM doesn't seem to allow negative track heights. If you enter a negative number in the elevation popup it gets converted to positive when the keyboard focus moves away; when you use Adjust Height > Edit Selection Start and End Heights again negative numbers are converted to positive ones.
I'm probably approaching this wrong, so... how should I (or RM) handle tracks that go below the baseboard? Adding an offset to everything (if I know my lowest point) would work, but it feels like the kind of thing a computer should handle automatically for me.
Currently the minimum height for tracks is 0 and can't be negative -
So I'm afraid offsetting all tracks by some amount to have the lowest tracks positioned at level zero as you've described is the way to go at the moment.
It's certainly a reasonable request and something on the to-do list to have negative heights.
There's also an open feedback ticket for this feature:
http://railmodeller.uservoice.com/forum ... ve-heights