I let the program fill them in automatically as "whole" rests.

JAV is correct, if the measure is empty. If you need the whole rest in (for example) layer 1, while there are notes in layer two, the easiest way is to use a tuplet: define the whole note rest as a 9-eighths in the space of 8-eighths, with no bracket or number showing. After you've done it once, you can copy it as needed.

In past versions, you could use the mouse, and click in a whole rest from the palette. For some reason, that isn't working for me, now.