Hey Firebar,
Boolean is a known 'problematic' and difficult way of cutting area's in an object, especially sophisticated ones.
* Make sure you are using a Editable Polygon to cut an 'Editable Polygon'. Dont use Editable Mesh objets on each other. Convert them first.
* Adjust the sophistication of the mesh of the cutting object with that of the Object being cut.
* Try moving vertices and edges around on the cutter to see if you can improve a cut.
* Make sure you have plenty of 'backup space' so you dont accidentally mess up your work. Backup, resave as next level up perhaps twice, just in case.
* Later, almost always, you will have extra Vertices in the cuts. I will move them over to the top of nearby Vertices and weld them. I use Side and then Top view to align a Vertice onto another one. When its dead on, I select both and weld. Might take a while, but its well worth it and leaves your model clean.
Also, try experimenting with Shape Merge instead of Boolean. I use Shape Merge all the time now. Its more stable. But you'll still need to clean up the Vertices after a cut. When cutting with Shape Merge, you will use a Spline to cut with. You can make a template part (exotic curved object) with a cylinder hit with Taper a few times, then make the Spline along its edges, delete the template part, and use the Spline as your Shape Merge cutting device.
NOTE: You can only do one side with a Spline. For me on my rig, they will not mirror for some reason, so I have to make a second Spline for the other side using the first one as a template, overlaying the vertices of the Spline over the other one, then move outward to where its hovering over the object to be cut.
Here is a quick Tutorial on Boolean, if it might help.
http://www.aerodynamika.com/cgi-bin/yabb/YaBB.cgi?num=1118866265
Have fun!
Bill