A rafter is the board that runs from the gutterline to the ridge of the roof. A truss is a premanufactured combination of the joist (the board that runs from gutterline to guttlerline) and two rafters to form a very large triangle with lots of little triangles inside it.
Cutting a notch is easy.
Cutting a notch with the correct angles and without taking to much material out of the rafter is not.
If you read some of my other posts, I would recommend buying premanufactured trusses every day of the week. Without seeing your project, I cannot say this for sure, but it may still be true.
They don't cost much and can be custom ordered for your project. Call some of your local truss companies and get bids.
Another option instead of notching the rafters is to purchase strongtie connectors made by Simpson. These are available just about anywhere you can buy a 2x4. Just explain what you are doing and they should be able to help you figure out which connectors work best. You will want to use broadhead 1.5" "joist hanger nails" with these. These nails are very strong and are made specifically for this purpose. DO NOT USE ROOFING NAILS.
Good luck, and rib your husband for leaving you with the hard part...