I am currently in the making of my pc and i was fairly new to it and i had screwed in my motherboard onto the flat part of the case, I had noticed that my case screws came with mounting screw but i did not use them, if i did use them i don't believe that my motherboard would fit the i/o shield and if i did not use them should i be worried for the solding pins touching the case
There are a few cases where the baseplate has 'moulded' standoffs, only come across it once or twice though. By far the majority use the little hex screw standoffs. It should be pretty obvious once you have the i/o shield in place and offer up the board. Usually there are a couple of springy bits to push against and just hook under. With the board against the i/o shield it should be perfectly flat and supported only at the raised points where the securing screws go through. If you have it pushed up to the i/o shield, run your finger down the edge of the board and the baseplate to back of the board, should be gap between them and it should be the same all the way round (if there is a gap at the i/o end and it tapers right down to nothing then that is wrong). Badly explained...but hope you get the idea!
I'd imagine that if they were supplied with the case then they are designed to be used, you risk electrical shorting otherwise.