The point of the plug-in is to produce well-styled printouts easily, just by using the dashboard settings. The dasbhoard settings are there to circumvent the need to edit css in the large majority of cases. They are your customised styling. They basically save your css edits into the database, and they won’t be screwed when you update. The printed output is consistent, whatever you do to your theme. However in some circumstances users need a little more tweaking and they can do this via the plug-in’s css file.
Whenever you make any edits to the code of a plug-in, it’s important to note down these changes as they will be removed by plug-in updating; the plug-in’s own css is no different.