Do NOT use Booleans!!!!
They're incredibly "messy" and often do more harm than good.
For your purposes, two techniques will likely be the ticket...
1) Knife: For any edges that are relatively straight, create an intersecting rectangle (or any NON-3D single surface polygon; so, it can be a disk or poly), position it with rotate and move along the exact path of the cut line and invoke the Knife tool (in the Tools menu). Starting in object mode, you first select the rectangle, then click the Set Knife button to make that rectangle the "knife object". Then, still in object mode, select the object to be sliced, and then click the Slice button. The line will be cut where the two objects intersect, provided both edges are traversed by the knife object. This may work for cockpit glass where the fuselage is "curved" but the line of the cut as seen from the top or side is "straight"
2. To further refine tricky paths in an object, I often manually create the paths by creating the vertices and edge lines. I use mostly the Insert Vertice and Slice Surface commands. I use these to create odd-shaped landing gear doors and bays in wings, for example.
First, you'll need to create vertices that are not already described in your mesh. Select any two vertices that are joined by a surface edge line. In Vertice Select Mode, select Vertice > Insert Vertice. A vertice appears midway between the two points. Then, select two vertices that are NOT joined by a surface edge line, and that have no edge interposed between them. Select Vertice > Slice Surface. Provided there are not already any intersecting surface lines, one will be drawn between the two.
Eventually, you can use these methods to "isolate" any shape within a larger object. Then you can cut that out, or change its material to glass... or whatever it is you need to do.
Send me a PM if you need more help in doing this. If you have Skype, I'm open to meeting with you online where we can share a screen, and show you exactly how to do this, as well as all kinds of things specific to building aircraft.