I’ve recommended Biblearc before as an excellent tool for tracing the flow of a passage (particularly one with knotty arguments, such as a NT epistle). I cannot praise it highly enough; it is an essential and early stage in my study of a passage. Arcing a passage brings it to life and helps me identify the train of thought to make sure I’m not importing my own onto the text!
That said, arcing takes a bit of time to learn, but it is absolutely worth it. The Biblearc team just announced a new online interactive course on Arcing and Bracketing (another method, which I have not tried). I learned via the training videos (still available on the site) but would have benefited from a more personal touch, like what they are offering now. Here’s some details and the enrollment page.