Hi Mac,
1.) That's right, making the inner side of the well low-permeable will mostly prohibit well-internal flow. Just keep in mind that a too high parameter contrast can make numerical problems; I usually use a parameter contrast of 100 or 1000.
2.) The flux-value on an internal boundary is applied twice, but no direction is given for the flux (meaning that the water does not have to flow with equal velocity in both direction). This applies for vertical BC (within a layer) as well as for horizontal BC (between two layers). In your case, the water will most probably flow in one direction only, you should therefore apply half of the calculated value to the BC. Don't forget to check the budget afterwards.