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I would be nice if your ISP explained why a shaper would preclude interface flaps.
If your Internet connection only provides X amount of bandwidth, which is less than what the physical interface supports, a shaper can be used to manage your available bandwidth.
To some of your other questions, you can only shape egress, although you can police ingress or egress. Normally, when using a shaper, you would use the "average" variant.
Many shapers don't appear to allow for L2 overhead, which often is what CIRs really describe. So, sometimes you need to shape slower than your nominal CIR bandwidth. (10 or 15% usually works well.)
