Learn French: Quel jean est-ce que tu préfères ?

In French, a pair of jeans is treated as a single item: un jean (masculine singular). Because the noun is singular, the interrogative adjective must also be the masculine singular form Quel.

How would this sentence change if I were asking about multiple pairs of jeans?

If you were asking "Which (pairs of) jeans" in the plural, you would use the masculine plural form Quels. The sentence would become Quels jeans est-ce que tu préfères ?

Why does the verb préfères have a grave accent (è) when the infinitive préférer only has acute accents (é)?

Préférer is a stem-changing verb. In the present tense, for all subjects except nous and vous, that second é changes to an è to match how the vowel sound changes when spoken.

Can I ask this question without using est-ce que?

Yes, there are two other common ways. You can use inversion for a slightly more formal tone: Quel jean préfères-tu ? Or, for casual conversation, you can put the question word at the end: Tu préfères quel jean ?