I have written a few articles regarding the various aspects of different packages. Keep in mind I wrote these when I was in my 2nd year of university so the title may be off but the information has been useful to thousands of people.
IC Packages Just lists some of the most common packages used for various parts. Some vendors, like TI, use these packages but will name them something else. Why, I don't know. This should probably be titled something else but it has helped many people nonetheless.
SMD Packages Also goes over some of the most common packages. This is a bold statement but I would say there are a much more diverse amount of SMD packages over IC and through-hole parts. So with that said, don't be surprised to come across a package you haven't seen.
These articles really just cover the different form-factors I guess. There will be variations across all of them, such as missing balls on the same size BGA, different pitch, etc..
When you move into your final design or you want to switch from development to a prototype, you can use either part you want. The SMD parts sometimes have different thermal characteristics, and are usually smaller than the development versions (another bold statement).
Which one you choose is entirely up to you and is based off of how you plan on assembling the next version of the product and how compact you want this product to eventually be.