Learn Russian: Я помню команду, которую мы встретили в третьей лиге. - I remember the team that we met in the third league.

We are using the Prepositional case to say in the league (в + Prepositional). The ordinal number третий (third) is tricky because it is the only ordinal that uses "soft" endings, unlike regular ordinals such as первый. For a feminine noun like лига, the Prepositional soft ending is -ьей, making it в третьей лиге.

How do we know to put который into the Accusative case (которую)?

The word который acts like a bridge. It gets its gender and number from the noun it refers back to—команду (feminine, singular). However, it gets its case from the job it is doing in its own part of the sentence. Since "we met it", it is the direct object of the verb встретили, so it must be in the Accusative case: которую.

Could I use the imperfective verb встречали instead of встретили?

You would only use встречали if you were describing a repeated action, like "the team that we used to meet all the time." Because this sentence refers to a single, successfully completed encounter in the past, we need the perfective verb встретили.

Why does лига (league) use the preposition в rather than на?