1) Play Kerbal Space Program, go into sandbox mode and try and build an airplane. You'll quickly understand what I mean.
2) Move them up a bit, or add more engines further up to balance things out.
That type of engine placement works for a boat because even at maximum speed gravity and boyancy are much stronger forces than the engines. Gravity keeps pushing the front of the boat down faster than the engines push it up and boyancy keeps the front and the back of the boat roughly at the same height.
In space, all you have are your engines. So if you have an engine on the far right turned on, it will push the craft forward and spin it. You need a second engine on the far left side to balance out that spin so that the craft only goes forward.
In this case the engine's midsection is about level with the bottom of the ship. Without engines above to balance things out that force will push the ship forward, and spin the ship with the front going 'up' and the axis being wherever the center of gravity is.
You have a lot of lee-way regarding the center of gravity btw, so don't worry about getting it exactly right. However you should expect about the same amount of mass to be above the engines as below. Similarly you'd need about the same amount of mass to the right of the engines as to the left... however your ship is symmetrical right to left so that isn't an issue here.
I think you have two good options:
Option 1) Remove the rear-most turret and move the rear launch area / bridge up. Then move the engines up so that they are a bit closer to where the rear launch area is right now. You can easily say there is some heavy stuff in the bottom of the ship to balance out the lighter weight towers and such that are on the top.
Option 2) Balance out the bottom of the ship by adding stuff. You can always add more stuff to the bottom of the ship to even things out. Turrets, launch bays, ect. It also may make sense to put some bomb-release gear there or some kinda moon pool.
