Ship templates go in the My Games\GC2TwilightArnor\shiptemplates folder (assuming you're playing TOA). Each template makes two files, one with an XML extension, the other with a SHIPCFG extension. Also see here for more detailed explanation and here for an example of a decent Terran ship template pack.
Personally, my preference is to use or build missile ship templates which allow for relatively easy mounting of missile weapons, typically in broadside configuration.
The best thing for that is to use the three-pronged style component on another component which has lots of similar and evenly-spaced hardpoints (red arrows) in a row. Place one missile on the end of the three-prong, and then adjust the direction of the three-prong.
By reversing the Z-axis on the three-prong you make anything on it go inside the hull, but by then reversing the Z-axis on the weapon you make the weapon component visible again, though now it pokes out from the hull. This doesn't work in every situation, but it does pretty well a lot of the time.
You can adjust the scale on the three-prong and the weapon component to taste, but obviously you don't want to do that for each one, so click the original component to set the right scale and facing before you place a new component of the same kind.
You may have done this already anyway but I thought it was worth mentioning.