I have a garage roof that has completely rotted. Pulling off the plywood sheathing, I see that the surface of the 2x6 rafters is rotted. This is a stupid question, but I can't figure out is how the rafters are attached to the center beam. I can't see any nail holes. Have I not looked hard enough? They can't possibly just be glued in. Can I just screw 2x4s into the 2x6s for a sound surface for the new sheathing or is it better just to cut and attach a new 2x6 next to the current one. If so, then how is the 2x6 attached to the center beam? See, I've gone full circle.

If only a little of the top of the 2x6 is rotted, it may be better off not replacing it. As you suggest, screw 2x4's to it to hold the sheathing.