The stronghold is one of most interesting aspects of Pillars of Eternity. You gain access to it at the end of first level, which means about 5-6 hours focused on the main storyline. One of the quests is about searching for someone called Maerwald. He resides in Caed Nua, in the largest building of the stronghold - the keep. To find him, you must descent to the dungeons, and then to first level of Endless Paths. Maerwald is in a closed room near the stairs. You will open the door by using high (at least four) level of mechanics or by finding a key that is in the room opposite to doors to Maerwald. You must kill three xaurips hidden in the corner of the room - one of them has the item you need.
After talking to Maerwald, the Steward of the Stronghold will decide that from now on you're the master of the stronghold. From that point, you unlock access to stronghold managing menu.
Stronghold is described by two indicators:
Prestige - shows how attractive the stronghold is for nearby citizens. The higher prestige level, the more often it will be visited by merchants and guests. It has impact on amount of taxes gathered as well. Sadly, larger prestige means that bandits will attack you more frequently.
Security - this indicator shows how well is your stronghold protected from bandits attacks. The highest its level, the less money will be stolen from the vault and less damage will be done by bandits attacks.