From the perspective of the user visiting the store and the admin managing the items in the back end you would see a single item that has multiple options. Most of the items options would be the same price, but a few will differ.
You can try this yourself as a test create a new item. Add an option type and make two option values for it. Now when you update that item select the first option choice and go to the price then set it to something simple like 10. After updating the item go back into this item to update it and select the second option. Now go to the price and update it to 11.
When you view this item on the front end you will have the choices for the options you specified. When you select the first option the price of the item will be 10, when you select the second option it will make the price 11.
In the background there are multiple products being created to handle all of the options but from the perspective of the user and the admin you would only see it as a single item with multiple options that affect the price. If this is not what you require please describe what you need in comparison to this so that I have a better reference for how this should be accomplished.