I have three secured cards and two of them have been over their limit by $6 & $11 once. Is this hurting my score?
Yep. If you don't have anything reporting over the limit, like a CO CC, or any current and active CC, and you take a CC over the CL and reports that way, you'll see a ding. IME, it was 10-20. YMMV on your credit. The damage completely goes away once the balance goes back in check. The 10-20 is aside from any util changes, IME.