I'm learning good topology best practices, and this course is so great for my purposes!
However I'm wondering when should I use one type of junction or another. Does this come with practice or something?
Glad to hear it! Sometimes junctions happen automatically (like with an inset) and it's just good to be able to recognize them. When I do need to use a junction intentionally it's generally because I need to connect one vertex to three or two to four when moving between low density and high density areas. When those situations pop up, which one you use depends on how many vertices you have to work with - generally only one will fit well.
Hope that helps!