It's very simple, every information about your account is kept server side. You don't even need to install the client using the CDs/DVDs, you can download it from the official website. Since you installed using the factions CD, you won't have to do that. The only thing important here are your access keys, make sure to merge them into the same account if you want your characters to be able to access both campaigns.
When you decide to start a new PvE character, you'll be asked in which campaign you want to create the character. As for traveling between two campaigns, once you get to the port city in your campaign (Kaineng Center for factions and Kamadan for nightfall) there will be quests available to take your character to the other campaign.
If you have trouble finding the quests, the wiki is your friend:
www.guildwiki.org