well, you can usually buy paper that has special cutout things, or is semi-cut, and it usually comes with software. then, to make the covers, your best option would be photoshop and then importing into that program. i dont know any programs that are compatible with all the manufacturer's different paper layouts. but there might be a program that prints guidelines for where you are supposed to fold to have a perfect fit, so that would have good results with semi-gloss paper to give you a very professional look. i dont really know any programs though, so someone else will have to step in here