OneNote: Align "Paragraphs" or maybe snap to a grid?
There isn't really an easy way to do this automatically, but OneNote does tend to snap to a grid when you move text boxes by hand, you just have to sort of "eye it" when it is snapping into alignment with other text boxes.
One other option is to enable grid lines in your OneNote view, which will help you eye it at least: On the Ribbon, go to the View tab, and in the Page Setup area, there is a Rule Lines option where you can choose a grid to be displayed of various sizes. You can also check to have your pages always created with these grid lines.
I have found a simple solution to this problem, which I was struggling with as well. When you single click below the text in the existing note container, OneNote wants to add the new text to the existing container. Clicking farther down, or somewhere else on the page then creates alignment issues, because OneNote doesn't really have an "align" or "snap" feature.
To avoid all of these problems and form a new container, just double click instead! And, if you want to make sure that the new container is aligned with the existing container, just double click over to the far left, and the new container will be positioned to the default, left edge.
Double clicking also works to insert a new container ABOVE the existing one, you just need to make sure that there is enough room up there to double click without accidentally clicking on the note date or the existing note. Again, doing your double-clicking way off to the far left helps there too.
There is a virtual vertical line on OneNote pages that if you click to the left of, the new text box will not go further to the left.
Let me say it in different words: If you type a title when you start a new page. Look at where the first letter starts, and try and click (or touch) further down the page to the left of that letter, this will bring the pointer at that level of the page, but perfectly lined up with the first letter of the title. Try it if not clear and see what this does.
I hope this works for you too.