I've done a gazillion of them, and also inset seams, and I still mark EVERY single dot on those freaking Y-seams.
I make an x by measuring a 1/4" just a little bit down each side from the point. And that x marks the space where I know I have to stop - I backstitch one or two stitches, where I have to join to the dot on the next block, etc.
But just do a couple to get the hang of it.