Hello Stefanie,
why do you want to use a 2nd kind (Neumann) bc for the well instead of 4th kind? Is it a large scale model just for the immediate vicinity of the well?
As for "both sides": the bc flux value is applied on both sides so the well will be pumping the defined amount of water both from inside and from outside the borehole boundary (same sign, no injection), at least if the inside of the well is also part of the model domain (no mesh hole).
Jochen