I'm not sure what you mean by squaring the center up?
One thing I do is place the block right side *down*. The block lies (lays?) flatter on the cutting surface this way. When I measure, I use the ruler markings lined up on a seamline (not on the cut edge). This greatly helps accuracy. If I can't line up exactly on a seamline but need to center the cut, then I center the ruler marking between seams.
Hope this helps some. Were you cutting multiple blocks at a time? That is harder!