How do the panels even work?
Lets assume the most naive idea, that the grav panel is basically a very big floor tile that attracts mass to its "top" side with a vertical vector that runs at a perfectly right angle to the surface of the panel.
Basically, what is above the panel is attracted to it. Things below the panel are not. Things sideways to the panel, even by a millimeter, are not.
Basically, above each panel, there is a theoretically infinite column in which things fall down on the panel, but its potency decreases with distance.
(DISCLAIMER: all of the above is absolutely silly, but this is the only way to have grav-panels that, aside from flagrantly disregarding physics, would not become an impossible engineering headache. Its impossible to have artificial gravity that does not violate physics, but lets alt least have one that conforms to basic common sense.)
So for simplicity's sake, lets assume the grav-panels are 1x1 meter, 1cm thick, and that anything in a realistic distance above them falls on them.
Therefore the most rational design, is to have the spaceship be a long tower, square in cross-section, with its bottom-most floor being covered in grav-panels, while the floors above the panels need not be. This way, most of the ship would be under 1g.
It might make sense to have the guts of the ship (engine, reactor etc) be below the grav-panels, "in the basement" so that they are in 0g (or not, this depends on how the engine and reactor works).
Another thing would be to have a "shaft" going through the ship that has no grav plate at the bottom, so that people and stuff could float up and down it in gentle freefall.
I would not risk putting panels on the walls, especially not opposite to one another. Intersecting gravity fields would play merry hell with the hull structure, and give everyone roller-coaster levels of vertigo, there is not need for that. You want the gravity to go one way and feel seamless between panels, otherwise your crew is going to vomit all over the carpet.
Now the trillion dollar question is: How much power do your grav panels need? And the multi trillion dollar question is, how powerful can you make them?
The reason I'm asking is that if you have artificial gravity plates that need less energy than they can create by making stuff fall down, yo do not need an engine or a reactor. You now have a device that can create its own energy out of nothing, and propel the ship at relativistic speeds. If you can turn a sequence of grav panels quickly one after another, and you stacked them so that their apparent grav field is substantial you can make the whole ship "fall" towards expelled bits of propellant, always missing it.
The same "multi-panel gravity" could very well be used as a weapon, maneuvering thruster (or rather, "puller") and a way to redirect enemy projectiles.