Lines at SFNE will most likely be pretty bad. I would say you should ride Cyclone in the back. Sure, it's rougher, but the rest of the coaster is rough without providing much of a thrill at all. At least the back has some great moments.
A few weeks ago before the schools got out, I had a good uncrowded day at SFNE. I had twelve rides on Superman, three on Cyclone, two on Mind Eraser, two on Thunderbolt, and one on Poison Ivy. Flashback was closed all day.
Last year when I went the second week of June, it was pretty crowded. I did three rides on Superman, two on Thunderbolt, and one on every other coaster. On a really crowded day, you might have to be content with one ride on every coaster.