Learn Dutch: Ga jij straks met de ov-chipkaart inchecken? - Are you going to check in with the public transit card later?

This follows the standard Dutch word order rule for the middle of a sentence: Time, Manner, Place (TMP). The word straks (later) tells us the Time, and met de ov-chipkaart (with the public transit card) tells us how you do it, which is the Manner. Time always comes before Manner.

Why is the verb ga instead of gaat here?

Normally, the jij form of the verb gets an added -t (jij gaat). However, in questions where jij or je comes directly after the verb, that -t is dropped. So it becomes ga jij.

Inchecken is a separable verb. Why isn't it split up here?

Separable verbs only split when they are the main, conjugated verb in the sentence. Here, the conjugated verb is ga. Because inchecken is the second verb, it gets pushed to the very end of the sentence and stays attached as a full infinitive.

What does the ov in ov-chipkaart stand for?

It stands for openbaar vervoer, which is the Dutch term for public transport. When speaking, you just pronounce the individual letters: O-V.