The software does support populating double side boards. The usual procedure is to have (only) small components on the bottom side, and populate and reflow that first. Then, supporting the board on low standoffs or similar, work on the top side. When the top side is reflowed, the bottom side solder melts again, but the surface tension of the molten solder keeps the parts on place, they don’t fall off.
NOTE: CAD packages may handle the data for bottom side differently that described here. Do check that the representation you get matches your intentions, especially for component rotation.
When the CAD data is loaded with the “bottom” check box ticked, the data is not loaded as is. Instead:
Since the board is upside down on the table, the origin goes from lower left to lower right. Therefore, the X coordinates are inverted. You should also set the board width for X offset (in addition to any other offset your data might have). This makes the machine use the origin in lower right and calculate X coordinates from the origin towards left.
Also, CAD programs (at least Altium) flip the rotation value when component is placed on the bottom side. Further, since you are now looking the board from bottom side, the rotation is to the opposite direction. This is corrected, so that the data you get matches to what you see.
NOTE: If you save the loaded CAD data, don’t check the bottom tickbox when loading the saved file again, you don’t want to get the above modification again.