File New Project is a well established action/command. If you are looking to replace it with your own, then I would guess you're in an RCP context, where you are free to do what you will. I would probably start with my own command, and then add it to the menu, toolbar, keybinding etc, as needed. There is an excellent set of tutorials/tips at eclipse-tips.
If you are writing plugins for Eclipse, the IDE, then you are almost certainly approaching the task from too low a level. In this case, I would guess you're wanting to contribute your own wizard, and things to come up when you right click in the package navigator view, under the New menu.
If this is the case, then I would go straight to the newWizards extension point,