There’s a lot to consider here. What I would do, is add a pair of ear level surrounds, and do 5.x.4 using the existing ceiling speakers as overhead speakers. Imo, Atmos is absolutely worth it, but you CAN NOT do it with bed layer speakers in the ceiling. If you can’t do ear level surrounds and center then do 7.1.
Also, what is the current subwoofer? The AVR can “compensate” for some things, but speakers placement and room anomalies can only be “fixed” so much. No you can’t use another zone to run the top fronts. As for XO, yes that’s set in the AVR. But if the XO is set higher, like 100hz, then you shouldn’t lower it. That’s because the AVR has found the f3 and set the xo accordingly. Also, there will be no Eq between the point the AVR set it at, and where you set it. In short, you can raise the XO, but not lower it.
Just .02 very quickly.