Hi Keith, well that's a pretty difficult type of shape to deal with so it can also be difficult to apply some of the "best practices" to it that you would normally try to do with simpler indentations.

Ideally when a main body shape is interrupted by a cut you would try to cut it using a large cutting surface which initially sticks out some distance past the body, and then use trimming or booleans to slice both pieces with each other - the cutting surface gets its excess parts cut off by the body and the body gets cut where the large cutting surface in turn gets cut by the body.

Something kind of similar to this for example, only with a curved surface as the cutting surface, formed with Network or Sweep:
http://moi3d.com/forum/index.php?webtag=MOI&msg=7138.6

But in order for that way to be used you need to visualize the indentation as a larger piece and focus on constructing it as one big surface, instead of focusing so much on starting with just cutting away pieces of the main body only by side profiles or whatever. When you are doing simple extruded cuts like drilling a hole straight through something it's easy to use a side profile as the cutting object which then if you do a boolean will leave the "side wall" surfaces in place inherited from the extruded 2d profile curves.

If you have something more complex than a straight cut you can instead build a custom surface and use the surface as the cutting object, that will then leave the imprint of the surface in your main body and your body will be cut into several solid pieces leaving each piece as a solid. The key difference with this way is that many of the edges will be generated for you as a result of intersecting the surface with the body - that's very different from focusing on just making those edges all by themselves to start with (using Trim or whatever), and then trying to patch surfaces in around those edges. It's difficult to get good surface quality by a patchwork of a bunch of individual little fragments just built next to each other, it tends to be better to have broader big surfaces that initially extend some distance out and then get trimmed back to form their final edge boundaries.

Hope that makes sense.... However, it could be possible in your particular case here that it would be difficult to form just one surface for the indentation since it might not follow one sort of guiding underlying broad form. If it has many different contours and bends in it then it becomes a pretty difficult thing to deal with in general and the regular best way of constructing it might not apply so much.

- Michael