During your first mission at Groom Range, you will be alone at the start. When you come across other surviving agents, they will join your squad, giving you two additional agents. You will then have a 3-man squadron for the rest of the game, with the exception of if an agent dies during a mission, and a few rare instances of a 4th agent supporting.
Once XCOM's central base is operational, you will have the option to recruit several additional agents (15 max possible, I think, I'll check next time I play. My last save is before the last action of the final mission, so I'd need to start a new campaign to get back to the base. --Xuncu 07:26, 28 August 2013 (EDT)). Another way to accuire agents is through Dispatch missions.
If recruiting from the Agent Management menu, the agents will start at Level 1, and you will have the option of selecting a "conditioning" perk which modifies character growth, such as a bonus when health is upgraded, or faster ability recharge. If an agent is a reward from a Dispatch mission, the Agent will already have a level or two (you are allowed to select all their Abilities), but you will not have the option of selecting the "conditioning."
Your squad will follow your movements, unless directed to move to specific locations. At the start of a skirmish (either when the aliens spot you, or you or an agent take a shot first), they will automatically go to the nearest cover; you should still go into Battle Focus to check on them, and change their position if there's a better spot for them to be. Similar to Enemy Unknown, they are under the rules of half and full cover (as are the aliens (except when Carter is the agent involved, see Tactics), so good placement is still paramount to victory. It helps to look around before a fight, as there are often routes to send an agent to flank aliens. Ultimately, familiarity with the maps will be your greatest asset in battle.
Left to their own devices, your agents will take their own initiative on firing their weapons, but will not use their abilities without being commanded to. And if they find themselves pinned and flanked, they will not move unless ordered to (you should, though: the damage received while moving will be less than being continually fired at from a flanking alien). Keep in mind that Battle Focus is not a "pause button": though time is vastly slowed, it is still a factor, aliens will be causing damage while you're Focused, and quick thoughts and actions are critical to getting you and your agents out of a jam. Agent Carter is also the team Healer, and his Heal ability works on the entire squad. This ability has a substantial reload time, so better to avoid using it when you can.
Health does regenerate as long as the agent isn't continuing to receive damage, and both health and abilities are fully recharged at the end of a skirmish. (at least on Rookie difficulty, I'll need to check on the harder ones)
When in Battle Focus, move the mouse to the left or right 1/3rd of the screen to move the camera to focus on the corresponding agent. If commanding them to concentrate their fire on a particular hostile, the display will also show the damage rate for a successful attack (a flanking shot will have +100% damage, ect).
Note that while your supporting Agents have unlimited ammo, they still obey the rules of clip size, and may be caught reloading at inoppertune times.