Don't mirror extruded features, only mirror bodies otherwise it will screw up your CutList (and maybe more?). Remember that you might not be able to get the correct Hole Callout (in the drawing) on any Hole Wizard holes on the mirrored body that existed on the body that was mirrored. Also, once you've mirrored a feature, the Mirror can only be modified to mirror other features...you can not change the Mirror Feature to instead mirror bodies, so you're forced to delete the mirror and put another mirror feature in selecting Bodies this time (the same goes for the vice-versa instance).
To leave an item out of the Cutlist...simply do not have the Solid Body in a CutList Item Folder. I beleave you have to turn the 'Automatic' option off to do this as well.
If using Structural Members, (multiple) 2D planes are useful to control the underlying 3D sketch (helps take out a lot of the clutter in the 3D sketch, and make it easier to modify later). Or you can use planes defined within the 3D sketch. Personally I still use the former methed (probably more out of habit).
In the drawing, use Relative View to get a view containing only one of the solid bodies.
This is more of a multi-body topic, but it might be worth mentioning...The Move/Copy Body feature is great for moving a solid body. I use it mostly for assemblies that I downloaded from the Internet and I did a SaveAs Part to them so I'd only have one part number to deal with in my BoM (like a purchased pneumatic cylinder or slide that comes in SW as separate parts for a body, rod, piston, slide table, etc..) But you never know, maybe you've gotten all the way to the end of your Weldment design and decide that one of the bodies needs moved, and you don't want to risk messing up all your existing relations, so the last feature could be to move the body over. As for the Move/Copy Body function itself, the Translate/Rotate method is best for moving a body a certain distance/angle (like extend cylinder 3"), whereas the Constraints method is best if you're trying to orientate a body relative to some other geometry (like move this body such that it's face is flat against another bodies face).
Later, Ken