Perhaps best to apply some last thing at night, so that you don't 'lose' it when going for a wee. I should think you could use it all over the vulva, urethra, clitoral hood, wherever you feel you would benefit. Not sure about internally though, nor about how long it would take to absorb. With a cream it would take a couple of hours to absorb the estriol. Anyway, I hope the oil works well for you.
Re the mild lower stomach aches, perhaps this is because you are touching a sore and sensitive area, and that is causing your pelvic floor to tighten (ie, you are getting a guarding reaction). I expect that will wear off over time.
Good detective work, Flossieteacake 😊.
JP x