Step By Step Diwali Pujan:

First clean the Puja room and then Bathe each Deity (Lakshmi & Ganesh) first with water, then with panchamitra/or rose water, followed by water once more
Now put Deepak (Lamp) in front of the Deities - As the tiny diyas of clay are lighted to drive away the shadows of evil spirits
Make a Panchamitra with 5 ingredients of milk, curd, ghee (clarified butter), sugar & Honey.
Place Few mithais, snacks & fruits as a prashad.
Make offerings of flowers, Abir (red colour), Sindoor (vermillion) and Haldi (turmeric). Light the Agarbatti (incense sticks) and lamps filled with Ghee.
Now make offerings of Fruit, Sweet dishes (mithai), Salty snacks (Mathis, Ghathia, Namakpare) and offer Dakshina (token money), which could be given to the poor. In the end offer paan (betel leaves), cloves. Now pray to the deities to seek their blessings.
Ganesh Pooja : Ganesh Puja is a must for Diwali Puja. (Lord Ganesha is to be worshipped in all pujas before any other God or Goddess.) (Ganesh Aarti is sung)
Laxmi Pooja : Place Lotus and other flowers at her feet as an offering. A silver coin is placed in front of the Goddess during the puja. Now perform Aarti with flowers in hand (Lakshmi Aarti is sung). After Deepawali Pujan have the Prasad and go out to burst Diwali Crackers.