Sending a convoy of troops to reinforce an ally's city will leave them there to fight and defend the city as their own troops, although that player won't be able to directly control them and you can recall them at any time you wish. They will also consume that players food supply will being garrisoned there.
You must also select the "allow troops of allied members to garrison your current city" option in the embassy to activate the garrison option.
Level 1 allows 1 alliance troop to be garrisoned.
Level 2 allows 2 alliance troops to be garrisoned, and allows you to establish an alliance yourself and perform joint operations with your allies.