This software is very easy to use.
One possibility would be to move the reference numbers of the top parts to the bottom silkscreen. I wish I could.
You can do that. By default the references will be on the top silkscreen layer for top components, but you can move them.
* First make sure the component references layer is on.
* Switch to component mode, zoom out, select all the components with the mouse, then choose 'Unselect bottom components' from the right click context menu. Now you just have the top components selected (in case you have components on both sides).
* Go back to the context menu and select 'Component references -> On bottom layer'. Now they will appear on the bottom silkscreen layer instead of the top.