Well, you have two scenarios and i'll explain each:
1) If you used your existing GW account (IE, used one of your PvP slots, etc): when you buy factions you add the brand new CD-key from factions to your existing account via the method Loviatar mentioned above. Doing it in this manner keeps your existing account, and add's factions content to it, and gives you an extra slot or two (number of added slots has not been determined yet).
2) If you choose not to merge the two accounts, you will get a chapter-2 only account with no chapter 1 content available, and 4 character slots. It can be, as this scenario implies, an autonomous stand-alone game by itself.
Having the ability to attach it to your chapter 1 account affords you the privledge of keeping all your hard work so far (unlocks, characters, etc).
The above two scenarios both assume you used a PvP slot on your existing account to play this weekend, and not that you used the free weekend key to make a completely separate account.
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