Habit.....I'm doing my first over-2 currently, where ever my needle is, I then skip one and use the next hole. Works for me. Do have to be careful though, sometimes the holes are smooshed and are not noticeable. I've only found one place that I did 1x1 and made the stitch the half size of what it should be. Luckly, it was in a spot that was easy to take out. Sometimes I miss the correct hole and one leg of the stitch is longer than the other, hopefully all those are immediately caught.

Look at it as a pound sign or hashtag or whatever you want to call it then count as many as you need to. Hope that's clear.

Oh, and I think this is one of the times gridding is very helpful. I did grid prior to starting. Took a while, but I think it's worth it.

The "link" below (you will probably have to copy and paste in your browser bar) has a good picture of what I would recommend for where to start your stitches. On step 3 it says: "You want to start your stitch next to a vertical thread that is passing over the horizontal thread just above your starting." PLEASE see picture in blog link below, in this case, a picture really is worth 1,000 words! This helps the stitches look good and also helps in your counting. If you ever find yourself starting a stitch not at the intersection noted above, you are at the wrong spot and need to recount. This has saved me MANY times working on linen or even weave such as Jobelan or Lugana. Good Luck! Nancy
https://stitchedmodern.com/blogs/news/how-to-cross-stitch-on-linen-fabric

Thank you
The pictures help