There are ways around this. First of all, you simply can't orbit Phobos (even at low altitude) because its weak gravity is entirely dominated by the gravitational field Mars close by. Essentially you're orbiting Mars with the same orbital period as Phobos, and slightly perturbed eccentricity.
To make landing easier you can create a vessel and place it on the surface so you have something to target, or better yet, place a prelude base from Dan's DG4 addon so you actually have something to land on which can also be targeted with the docking MFD. :thumbup: