If my food doesn’t come out quite done enough, next time do I raise the temp or extend the time.
Raise the temp
Depends what you mean and what you are referring to, without more info, it’s hard to give you an answer.
Let’s take chicken breasts for example…
You’re cooking at 140F for 45-60 minutes. They aren’t quite done, probably want to raise the temp a few degrees.
Now, how about a beef chuck roast
135F for 3 hours and it’s still tough. Chuck has a lot of tough fibers that need time to break down. Cook it another 10-12 hours and then get back to me. 
BTW, did you check your temp calibration? The Anova could be running a few degrees lower than what it displays / thinks it’s running at. This could cause food to be undercooked as you describe.
Thanks for your help, will try.