My husband used to have long hair (years before I knew him; he looks so different in those old pictures!!) He says that he would just pull his hair back before putting on tefillin.
OK, well those (and as far as almost all kippas that I’ve seen) are worn on the top and back of head, not the forehead, where the tefillin go. I’m not sure what’s the question.
The yerushalmi kappelach are not at all like the NaNach headgear. Not on shape size or way they are worn. The NaNachs are more similar to the Bucharian yarmulkas in size and shape.
And it’s not a “few” chasidim. The Yerushalmim wear them. They put on tefillin just like anyone who wears a normal sized yarmulka does. A better question is how do those who wear tiny little kippot put on teffilin, they have almost no head covering at all.