Mater infantem iubet in cubili cubare, quia nox obscura est.

We know from its form and from the verb.

• mater is nominative singular, the case usually used for the subject.
• iubet means he/she orders, so we expect a singular subject.
• Since mater is nominative and matches the verb, it is the subject: the mother.

Infantem is accusative singular. After iubet, the person being ordered is put in the accusative.

So:

• mater = the one giving the order
• infantem = the one receiving the order

Also, with iubeo, that accusative noun is understood as the subject of the infinitive cubare. In other words, it means the mother orders the child to lie down.

Because iubeo commonly takes an accusative + infinitive construction.

So:

• infantem = accusative
• cubare = infinitive

Together they mean something like the child to lie down.

This is a standard Latin pattern after verbs like iubeo:
Mater infantem iubet cubare = The mother orders the child to lie down.

Because iubeo usually does not need ut. Latin typically uses the accusative-and-infinitive pattern instead.

So Latin prefers:

• mater infantem iubet cubare

rather than something built with ut.

This is different from some other verbs of commanding or urging, which often do use ut + subjunctive.

Because in can take two different cases:

• in + ablative = in/on a place, showing location
• in + accusative = into/onto a place, showing motion toward it

Here the idea is location: the child is to lie in bed or on the bed, not move into it as the main grammatical point. So Latin uses the ablative:

• in cubili = in/on the bed

Cubili is the ablative singular of cubile, a neuter noun.

Cubile means a bed, couch, resting place, or place for lying down. In this sentence, in cubili cubare gives the sense of to lie in bed or to go lie down in bed.

Yes, they are related in meaning, but that is perfectly normal in Latin.

• cubile = bed / resting place
• cubare = to lie down / recline

So in cubili cubare is literally something like to lie down in the bed. English might avoid that kind of repetition more often, but Latin is comfortable with it.

Because obscura is an adjective agreeing with nox.

• nox is feminine
• singular
• nominative

So the adjective must match it:

• obscura = feminine singular nominative

That is why we get nox obscura est = the night is dark.

Quia means because. It introduces a clause giving the reason for the mother’s command:

• quia nox obscura est = because the night is dark

So the sentence has:

• a main clause: Mater infantem iubet in cubili cubare
• a reason clause: quia nox obscura est

Latin word order is more flexible than English word order. A verb often comes near the end, especially in simple statements.

So nox obscura est is a very normal Latin order. Latin could rearrange the words in other ways, but the endings would still show the grammar. The ending position of est does not make the sentence unusual.