I am totally new to Java and the Eclipse IDE - and not that experienced with programming generally - and I am currently enrolled with two online uni courses, both of which use Java (Algorithms 1, Stanford and Introduction to SAP HANA Cloud Platform).
I have already created the SAP workspace, and left the 'always use' box unchecked.
Are there any issues I should be aware of if I create a different workspace for the Stanford course? Is this even an advisable thing to do?
I would recommend that you use the same workspace, but create a separate "Working Set" for each of your courses. This way, you can share the same eclipse default settings between all your projects. A Working Set can "contain" multiple Projects, and you can decide exactly which Working Sets you want to be visible at any time (simultaneously in the same eclipse session).
On the other hand, using different Workspaces, you'd have to manually tweak all the default settings yourself every time you create a new Workspace. And if you decided to change a default setting, you'd have to manually do that to every Workspace.
Using Working Sets is much easier and more lightweight than using Workspaces. You stay in the same eclipse session when creating a Working Set or switching between them. Also, you can see and work with multiple Working Sets at the same time in the same eclipse session.
Here is a brief article describing how to set up Working Sets.