I've screwed in 5 of the 6 screws on my motherboard. The last hole isn't accessible for some reason, as it is slightly off centre from the standoff. Will that be a problem or can I leave it like that?
In case you can't place the screw in even after you've done what ronintexas said - remove the standoff in question and leave it removed, you'll be fine just don't let the standoff there without a screw in.
Loosen the other screws about 1/2 to 1 turn, and this should allow you to reposition the mobo to get it aligned properly. Then tighten all screws (DO NOT OVER TIGHTEN).
In case you can't place the screw in even after you've done what ronintexas said - remove the standoff in question and leave it removed, you'll be fine just don't let the standoff there without a screw in.