I'm configuring a rectangular zone for launch site and using Zone Manager and Dynamic PvP plug-ins.

I've configured the Zone Radius to 0.0 with X=700, Y=350, and Z=400. I can do /zone_edit to see the box and get the warnings in the right place but the rectangular box has no color to it and can't be seen.

I've also tried adjusting the Dome Darkness down to 0 to see if it disables the dome  to activate the rectangle but no luck. What am I doing wrong?

Domes and colored rings are only supported for spherical zones. This is a game limitation, as Facepunch doesn't provide any cuboid entities.

This means you need to choose between visible spherical zones, or zones that fit the geometry of the monuments. Personally I go with the latter, but it's an easy choice since immersiveness is a goal on my server.