I have 3 or 4 decent aviation only planes; or at least so I think? You can maybe take a look at how I set them up if you like. Just follow the "My Designs" link in my signature below.
I generally follow these rules...
I display the center of balance and center of lift gadgets and basically try to keep COB slightly ahead of COL. If these two get reversed at any point during your flight the plane is gonna be difficult to control. When you let off the throttle, the plane needs to fall nose first to the ground.
If I'm looking for performance or a VTOL jet, then thrust to weight ratios are also of interest and I like the Engineering Redux mod for this info, TWR of 1.0 or higher tends to be a funner plane to fly.
For runway tracking I'm looking to maintain pretty close to a center track until the recommended rotation speed. I find that I can usually fix and/or improve runway tracking by:
First and foremost make sure all of your gear are attached at a perfect 90° before moving them around. ...and some of the Mk2 fuselages seems to be notoriously bad as anchor points in this respect. ...and let's not even discuss a Mk2 fuselage radially attached to another Mk2 fuselage, you have to attach these things where the wings mount at perfect 180° and use the offset gadget to move them carefully into their final position or they compound error and translate it into what you think are well placed landing gear. Somtimes to shore up the tracking, I might attach the gear where you might attach a wing, and then rotate it 90° and carefully move it around with the offset gadget. Many times, this solves the problem. Sometimes I allow some rotation on the main gear, but usually not more than a 10° to 15° camber.
Next I would look to increase the distance from forward gear to main gear. Move your forward gear all the way out to the nose; maybe past the nose even. If it still won't track, I have to maybe consider a redesign at this point. If it does track, then I start moving the forward gear back to see how far I can go before it gets loose again.
Mechanical Intervention - Dual vertical stabilizers, and maybe a couple small ventral fins get added as design modifications first. I've used split flaps in some of my designs (the FE-03 for instance) to create additional drag toward the rear of the aircraft to help stabilize it during takeoff and landing. ...or even forward split flaps to help increase lift. Speed brakes may be another option in this respect, and can also be used for additional yaw control. But typically, it's more related to the first and second bullet above.