When performing a dent fix type of auto repair project, the position of the tool, known as a dolly, will depend on the type of dent and which direction the dent goes in. Normally, if the dent is relatively small and gradual, you will place the dolly on the opposite side of the dent, and hammer against the dent itself. In other words, if the dent is pushed inward, you will put the dent on the outside of the body panel and use the hammer on the inside of the panel. You will want to try and work the dent out in sections normally, instead of trying to remove it all at once.
For more info, see Car Dent Removal Techniques that Work