First and most importantly: make VERY sure that there are NO metal standoffs under your mobo in a spot that does NOT have a mounting hole in the mobo. Mobos are designed to be grounded to the case at each mounting hole, but at NO other points. So a standoff under the mobo at a wrong place can ground out a mobo trace.
Next, as you line things up, remember that the custom metal rear panel that surrounds the mobo's external connectors needs to be in place with the connectors fitting through their holes. Be careful that the springy fingers around each hole go OUTSIDE each connector's shell - I once found I had a finger sticking inside and shorting out a connector pin.
Last, and this may help: most cases come with standoffs pre-mounted in "common" locations. But you will also find other holes drilled and tapped in your case bottom for alternative standoff locations. The idea is to customize it yourself. You unscrew any standoff that does NOT line up with a mobo mounting hole, and re-locate it to the proper pre-drilled hole. Ideally when you're done there will be a standoff beneath each mobo mounting hole, and absolutely NONE where there is no mobo hole. You might even have a spare standoff or two left over, and that's OK.