Homebrew PCBs

Most pcb programs assume holes are through plated which isn't the case
when I make my own double sided board.  Do you guys usually solder
both the top and bottom of a pin that's through plated?

If anyone is using Eagle, in the Single Sided demo, whenever I
autoroute it, it knows to generate wire bridges for the top layer.

I use the same CTL file but whenever I generate my own board, it seems
to assume plated through holes.

I checked the DRC and they seem to be the same.

How do I get Eagle to treat the board like in Single Sided demo and
not plated through holes?  Thanks.
Henry