During the late 16th century, both organizations maintain hidden networks throughout the Polish-Lithuanian Commonwealth.
Wilno is particularly valuable because of its political importance, trade connections, diverse population, and proximity to vast forests and important roads.
The Assassin Brotherhood uses Wilno as a base for gathering intelligence and watching influential political figures.
The Templars seek influence among powerful nobles, military commanders, merchants, and political factions. They attempt to shape events without revealing their existence.
Neither organization openly rules Wilno. The city's ordinary inhabitants continue their daily lives largely unaware of the secret conflict surrounding them.
Kraków is the main city Templars stay in. They use it as a base of operation, it's very hard to get close to as an assassin not mentioning getting inside.
Assassin's didn't yet create a base of operation per say. They work in different cities and towns trying to establish some foothold in the country as the organisation got here not long ago.