Under-filled bars
If you are working in, say, a bar of 4/4 time and only write two beats’ worth of music, StaffPad doesn’t assume that the other two beats should be rests. Rather, like a sheet of manuscript paper, those beats remain totally empty until you complete them with rests or more notes, or change the time signature. These are called underfilled bars.
StaffPad, of course, is more intelligent than a sheet of paper, and will color underfilled bars gray. You can decide what to do with them at any time, or let them be.
Underfilled bars can be turned into proper pickup bars; see Pickup bars.
Over-filled bars
Similar to underfilled bars, overfilled bars are bars with a total number of beats exceeding the prevailing time signature. Overfilled bars are colored red, and it is up to you how (or if) you wish to resolve them.
The nice thing about this approach is that you can write music first and change the time signature later, should you wish. More in Time signatures.