X3: Albion Prelude is an Add-On to X3: Terran Conflict. Using X3: TC as a basis, many improvements were made to the engine and other areas of the game. To limit its download size X3: AP will share files with X3: TC where it's possible. This means that a complete X3: Terran Conflict installation is needed to be able to install and play X3: Albion Prelude. X3: AP is treated as a separate game, with different folders for savegames, screenshots, control profiles etc. Even after installing X3: Albion Prelude, X3: Terran Conflict is fully playable and moddable. More on Mods below. Due to the major changes between X3: Terran Conflict and X3: Albion Prelude, savegames are not compatible.
Who gets the free version and the discounted versions?
Anyone with a Superbox will be able to download X3: Albion Prelude from Steam for free. Anyone with an X3: Terran Conflict version (this includes bundles like X3: Gold) will be able to buy X3: Albion Prelude for the 'Add-On' price of €9.99. If you have a Non-Steam version of either the Superbox or X3: Terran Conflict, you will have to register it with Steam before.
http://www.rockpapershotgun.com/2011/12/15/x3-albion-preludes-sumptuous-spacestuff/