Either side stays covered up unless you're doing corn. Found that with them uncovered you'll overload the shoe in cereals and canola. If you don't have large wire concaves you could pull wires and leave the last two on either side as a large wire setup and it will help drop the crop out faster instead of carrying it to the back.
i would be more worried about overloading the sieve by removing the grate covers.hopefully you will have 99% of the wheat and mog seperated by then. they do overload the right hand side because of overthrashing. there are so many variables to consider it's a tough call. some variaties of wheat are easy thrash and some are horribly hard to get a clean sample. we grow brandon which is thrashed out by the front beater. if you have to start seperating grain from mog at the rear of the grate your in big trouble! my way is to thrash it out of the head in first two concaves and seperate it out of the mog with the last series of wide spaced concaves.past there i would hope that 95% is on the sieves.