If you still struggle with marking centerline correctly try using a 'Centerline Finder'. You'll find that this handy tool will take the guesswork out of joining tube.
How is a Centerline Finder used in notching?
A basic notch starts with laying up the tube where you want the joint. Temporarily secure the tube so it can be marked and placed into the notcher.
Position yourself to view both tubes at the intersection from a right angle perspective so you can accurately mark both the centerline of the tube (to be notched) and the intersecting point(s). The more accurate the marks - the better the resulting notch will fit. What is important to know is that as long as the centerline of the tube to be notched is correctly marked in relation to the joining tubes - your notch will come out correct.