Flat-roof only has a small area that leaks. Two on the boards have rotten away. Area is about 4 x 6 feet. Problem is the roll roofing
comes in such large rolls $75.00 . I don't think Home Depot will just cut a small patch out. What are the alternatives?

Roll at my local HD is $43.. Check with local roofing contractor to see if they will sell you a piece.