Learn Russian: Где рукопись, которую вы нашли вчера? - Where is the manuscript which you found yesterday?

The word который (which/that) gets its gender from the noun it points back to, but its case from what it does in its own part of the sentence. It points back to рукопись (feminine), so it must be feminine. In its own clause ("which you found"), it is the direct object of the verb нашли (found). A feminine direct object takes the accusative case, making it которую.

How can I tell that рукопись (manuscript) is feminine?

Nouns ending in a soft sign (-ь) can be either masculine or feminine, so you often have to memorize them. However, words ending in -пись (like подпись for signature or запись for recording) are feminine. Also, seeing которую right after it in this sentence gives away its gender!

Why is there a comma before которую?

In Russian grammar, you must always put a comma before a relative clause—the part of the sentence that starts with words like who, which, or that (который, что, кто). While English often drops this comma, Russian strictly requires it.

Why is the verb нашли used instead of an imperfective verb?

Нашли is the past tense plural form of the perfective verb найти (to find). It is used here because finding the manuscript was a single, successfully completed action that happened yesterday, rather than a continuous or repeated process.