The manual for this case is not very clear, although it does indicate that it comes with three brass stand-offs like Yogi showed. Now, 3 is not enough, but think I know what's gong on here.
There are several slightly different mobo sizes and designs. MANY are "full size" and include nine holes for mounting screws - 3 in a line each at the top and bottom edges and one line across the middle. Other boards have a slightly different layout of holes. If you look closely at your mobo and find those holes, you will see that each of them has a small "star" pattern of metal contacts around the hole. The mobo is designed to be grounded to the case by the mounting screws at these points ONLY, and nowhere else.
Your case appears to have pre-mounted standoffs in those nine points of the case - the "bumps" you mentioned. But it also comes with three "spare" brass stand-offs for you to use if your mobo needs a mounting spot at a different location. For those you would probably use a pre-drilled hole in the case bottom to mount a stand-off.
The general rule is this: Your case should have stand-offs mounted under every mobo mounting hole if possible, BUT it should NOT have any stand-off in a spot where there is NO mobo mounting hole to match. So examine your mobo and case carefully. Gently place the mobo alone into the case and check the alignment of mobo holes with pre-installed standoffs. If they all match up, you're OK with no problems. When you actually get to the point of attaching the mobo to the case, you will just put the proper screws through those mobo mounting holes. IF you find that a mobo mounting hole does NOT line up with a pre-installed standoff, you may want to use one of the brass spares to provide the attachment point there. IF there is a pre-installed standoff where the mobo has NO hole, see if you can remove that pre-installed item so it does not touch the mobo bottom surface.
I cannot tell for sure, but the photo you posted MAY indicate an interesting feature. The nine pre-installed standoffs which you call "bumps" appear to be plastic rather than brass. MAYBE they are plastic on the outside and top to prevent electrical contact with the mobo bottom. BUT maybe they also do have metal inside them where the threads are for screws so that actually using a screw would provide an electrical connection, but not merely by surface contact. Of that's the case, those "bumps" may be permanently mounted there and designed so that it is not necessary to remove unused ones.