Welding is the best method, although i have seen some guys do a really good (although really ghetto) job using JB weld, and i would NEVER recommend it because it won't last and could potentially break up, leaving the engine bay looking worse than it did when you started.
I will say if you try to weld, practice on something else before you hit the car. If you weld too much or too crappy, you're going to have to grind all the access off, and that makes smoothing it out a huge PITA. My buddy is doing this right now and if you really want the sides to be smooth, it takes a lot of work, lots of body filler and you're going to be filling/smoothing/filling/smoothing over and over to make it look right.
Oh i'll also add, the easiest way to make it look super good is to find the precut panels that you weld over the sides. I know someone on here had some that i think someone on Corral was making. My buddy cut/made his own out of sheet metal which is another option.
