you square your top by making sure your edges are straight- sides and top/bottom===the quilt is generally trimmed/squared after quilting- but needs to be straight for long-arm quilting so when it is loaded on the rollers it rolls up straight- otherwise it will (feed) crooked and you could run out of batting/backing--generally if you trim/ keep things straight as you create your top- it will be straight enough for quilting
about the gray thread---light gray on light fabrics, dark gray on dark fabrics---blends in and pretty much goes with anything---keeping you from having to change thread colors all the time- if you simply use a (neutral) like gray- it almost disappears.