(1) How do I cut an object into two separate objects? For instance, if I create a cylinder, then I knife the cylinder in the center. How do I break up that cylinder into two separate objects at the part that I knifed?
Select all the faces of the part to be separated, then press "Move" to make the Arrow Handles appear. Press Ctrl+C to copy the selected area, then press Ctrl+V to paste. This will copy the faces and paste them in exactly the same place as the original faces, so it will look like nothing changed. THEN move the Arrow Handles; you will see the copied/pasted faces move separately from the originals. Move them temporarily out of the way (above, in front, or beside the originals; use only one direction), and delete the original faces from which you made the copies from. Your cylinder is now two separate cylinders.
(2) How do I do a 'cookie cutter' like operation? Let's say I already have a fuselage. I want to attach a side intake. To do that, I'd start making a box. Then I'd slap the box onto the fuselage. But I'd want the inner side fo the box to adjust to the contour of the fuselage.
Turn on the Pt, Ln, and Fc buttons in the upper left corner of the Drawing Area. Move the intake box into position, overlapping with the fuselage. Take note of the positions of the vertices around the overlap, and the vertices of the edges of the inner side of the box. If necessary, turn the Fc button on or off to be able to view them separately; at minimum you will need to see the points/vertices and lines. Press the Del button on the Edit Control Panel, and delete each face on the fuselage with which the intake's shape overlaps, so that you make a large hole around the intake's sides. This is to identify the area of the fuselage from which the original shape will blend into the intake.
Then, press Create on the Edit Control Panel, and make new faces that connect the surrounding vertices of the hole around the fuselage with vertices on the intake. Just position the cursor over each relevant point until it changes color, then press, then move on to the next point. This makes new faces in the fuselage that connect with the shape of the intake, thus making former's shape conform to the latter. After completing the operation, separately select each one of the vertices that form the new faces, and press Ctrl-J to join any vertices that may not be exactly aligned and make sure that the indented area can be unfolded by Pepakura without breaking up into individual new faces.