Its Ok if the Motherboard flexes a little it's bound to do it. What you need to do is find a nice screwdriver that fits into the retention clip nice and snug, if you use one thats too small your are likely to slip and damage the board. Once you have found one that fits nice and snug push the clip straight down and lever it back very gently, and only lever it back a tiny bit, be carrell and take your time, once you have done it a few times you get more confident and you just do it naturally without thinking about it.
If your a little scared about stabbing the motherboard put down some soft material around the area where the screwdriver is likely to hit if you did slip. Dont use someting like a cloth though it may cause static damage, what I would use is something like a small piece of cardboard or somewhere along those lines.
I would leave the Motherboard in the case because if you take it out it could slip on the surface, where as if its in the case its in tight and not going anywhere.
Remember take your time, and concentrate watch what your doing and if you dont feel confident enough to do it you can always ask someone else to do it!