If you are using Goodnotes 6 and Classroom, you may be wondering whether you should be using the same account on both, or have 2 separate ones. You can use Goodnotes 6 as well as Classroom, you don't have to choose! You can refer to this article for more information on this and what you might use each one for: How is Classroom different from Goodnotes 6?
Goodnotes 6 and Classroom are two separate apps, so regardless if you use the same login details, your files will not sync between them. You may wish to manually move your existing Goodnotes 6 documents over to Classroom, which you can do by following the steps in this article.