Depends on what are you looking for, if you want just to quantify transcript expression in your annotation or if you want to also identify novel transcripts or isoforms. Choose the one that fits your questions.
Why are you using StringTie in the first place? Not that it is a bad tool but you should only use it if you are interested in specific questions. Take a look at this section of my vignette which describe tools to use for quantifications in different circumstances.