You can work in inches, centimeters, or millimeters. The units for a particular plot are specified in the "Units" popup menu near the upper left of the window, and you can set the units to use for all new documents in the preferences under the Edit menu.
Most values you enter will be interpreted in the chosen units, with a few exceptions. In general, the program expects decimal values in fields. The program respects the number format specified on the computer it's running on, so for instance French users should use commas instead of periods for decimal separators.
For most values, you can also enter fractions directly, by including a slash (/) in the field. For instance, you can type "1/16" instead of .0625.
For values that can be specifed as percent of chord (notably spar/reference line positions), add a percent sign (%) after the value.