It should be as simple as bolting it all down to the qcw. Bolt it down and run a test cut. Don’t worry too much about square for now. Just get some successful cuts under your belt.
Like support said, get a few cuts done. If you want to do a webcam stream and live chat I can walk you through the steps that I did to get my machine pretty close to square. How do your corner to corner measurements look when the machine is bolted to the qcw?
Jaycob, although I doubt this is a contributing issue, you may want to make sure the QCW is square before looking at the CNC itself. Weirder things have happened!