Well, here's how you'd do it not too fancy.
Take your skill,the name of the thrown item. Name it that ( the actual items name of course). The icon doesn't matter, nor does the description, nothing matters except for Scope, target animation, common event, and the stat stuff at the bottom. Scope should be 1 enemie or all enemies depending on which you want.
Target animation is a little hard- press apply, then X out and see if you have a picture of what you want the attack to look like (such as a throwing knife or whatever.) If you do,go back to database and go to animations. If not, go to material base and import whatever it is you DO want into the animation graphics folder.
On animations, make on titled the name of the thrown item and choose the animation graphic as the desired pic. Then, click on the #001 under the back button. Select the picture of the whatever at the bottom and click on the picture where you want the animation to start. Create a new scene (that is what these are) and put the pic in the spot you want it to go to next, etc etc till you have your desired animation. then, apply, then go back to skills. Add the new animation as your target animation, the apply and go to target Common Event (the tab at the top)and input this:
Then go back to skills, make a new one named throw and set everything on it so that it is blank and does nothing, but make common event the one you just made. Then make the thrown item. And you're done.
Here's what it'll do:
You open a chest and find "Rising Sun" (thats my thrown item name) and get into a battle. You're character uses Throw, and then it'll say thrown up top, then it'll say Rising Sun and attack. If you did not have Rising sun, it will say "Throw Failed."
Helped?