Test the main functions of your system first. My software, the most important piece is making sure reps can enter calls they make to Doctors. This is just an example. Don't worry about cosmetic issues, I.E. spelling mistakes. Pretty much make sure all the main functions work, then if there is time, go a little deeper.
I agree with the statement above, but more specifically look into a risk based approach. It is not always the main functions that will cause your organization heartache in the end. Look at the functions that pose the most risk, what is new, what are the most customer used functions, and of course the main functions.