How do people make sure that their wheels are 'flush' with fender flares?

I went through a lot of this with my Javelin. The best way is to have a wheel which you know the specs of (backspacing/offset and width), and test fitting it. From there, you can measure how much farther out you want your wheel to sit. This can be done with buying wheels at a certain offset, spacing with shims, or spacing with bolt on wheel spacers (or a combo of offset and a spacer for fine tuning). Tire width also plays a role.

I run nearly the same set up as the shot you’ve posted. It takes plenty of measuring, asking around and calculating. In my case, I mounted the flares first and then measured from the hub out, then confirmed the width and offset I’d need by mounting up a smaller wheel that I knew all the dimensions of, and seeing if the deficit between what I had and what I wanted all squared up.