For automated welding the first hurdle is keeping your parts accurate enough. Humans can account for misfit parts, machines can't. The next task is properly fixturing the parts. Automation won't change the basic properties of the type of welding you are doing; if you couldn't weld vertically with the material/filler that you are using when welding it by hand automation won't change that.
For seaming there are two basic type of fixturing. One uses a continuous series of fingers on each side of the seam that hold the material down and in registration with each other. You close one set of fingers, run one plate up against them to square it, and then close the other set on top the inserted plate to hold it in place. Next you open the first set of fingers and push the second plate up to the edge of the first and then close the fingers on top of it. This should give you a pretty straight seam but some tracking adjustments might need to be made depending on length. Many times this is done manually with a joystick, etc.
The second basic type is used for situations where the seams are less perfectly aligned. It uses some sort of seam tracking to keep the torch on track. Seam tracking devices can vary from laser tracking, to mechanical probes to through arc seam tracking (with specialized equipment.)
To control the welding process you will need to at least sense that you have established and maintained an arc (similar to plasma cutting). Some newer welding power supplies will have an output for this. If you don't have one you can use a current sensing relay. You will probably also want to have better control of the gas flow if your going to do it a lot. That way you can turn the gas on a second or two before starting to weld (pre-flow) and keep it on several seconds after the weld (post-flow). Fancy welding controllers will also let you set different current profiles for starting and finishing the weld.