When I was renting time on a LA, the lady that trained me told me that when she gets an unsquared quilt she can do an all over pattern (with the computer) and simply adjust the pattern for the uneven portion when she gets to the bottom. To a judge's eye I'm sure it wouldn't be acceptable, but to the average person I'm sure they don't even notice if the pattern is a bit wider or longer at the bottom. I don't know if this would work for waves, but if it's pulled a little tighter as it's being quilted, maybe?
I don't measure in the center or on the ends. I use a piece of border that's longer than the top and cut it off to square when it's sewn on. If I'm doing a patterned border I'll pin it so it's just right. I have a Pfaff though, so maybe the IDT helps? I've been told by my trainer (who does lots of people's quilts) that my quilts are unusually squared and perfect. Ha! what a silly lady!