Moja siostra chowa dwanaście flamastrów do pudełka po lekcji.

Because siostra is a feminine noun, and the possessive adjective my must agree with it in gender, number, and case.

• moja = feminine singular nominative
• mój = masculine singular nominative

Since siostra is the subject of the sentence, it is in the nominative, so we get:

• moja siostra = my sister

Chowa is:

• 3rd person singular
• present tense
• from the verb chować

It agrees with moja siostra, so it means:

• she hides
• or, in this context more naturally, she puts away

In Polish, chować can mean both to hide and to put away/store away, depending on context.
With do pudełka (into the box), the meaning is clearly puts away into a box.

After the numbers 5 and higher, Polish usually uses the genitive plural form of the noun.

So:

• jeden flamaster = one marker
• dwa / trzy / cztery flamastry = two / three / four markers
• pięć, sześć, ... dwanaście flamastrów = five, six, ... twelve markers

That is why you get:

• dwanaście flamastrów = twelve markers

The form flamastrów is the genitive plural of flamaster.

Flamaster usually means a felt-tip pen, marker, or colouring marker, depending on context.

So dwanaście flamastrów could be understood as:

• twelve markers
• twelve felt-tip pens

In everyday learner-friendly translation, markers is perfectly fine.

Because the preposition do always takes the genitive case.

The base form is:

• pudełko = box

But after do, it changes to the genitive:

• do pudełka = into the box / to the box

So:

• pudełko = nominative
• pudełka = genitive singular

This is a very common pattern in Polish:

• do domu = to the house/home
• do szkoły = to school
• do pudełka = into the box

In this sentence, po means after, and with that meaning it takes the locative case.

The noun is:

• lekcja = lesson / class

In the locative singular, it becomes:

• lekcji

So:

• po lekcji = after the lesson / after class

This is a fixed and very common structure:

• po obiedzie = after lunch
• po pracy = after work
• po filmie = after the film

Here it is locative.

That is a very good question, because many feminine nouns have the same ending in different cases.
For lekcja, the form lekcji can appear in more than one case, but after po meaning after, it must be locative.

So in this sentence:

• po lekcji = after class
• case: locative singular

You can tell the case from the preposition, not just from the ending.

Polish does not have articles like English a/an and the.

So:

• siostra can mean a sister or the sister
• pudełko can mean a box or the box

The exact meaning usually comes from context.

In this sentence:

• moja siostra already makes it definite enough: my sister
• do pudełka can be understood as into the box or into a box, depending on context

This is completely normal in Polish.

Yes. Polish word order is more flexible than English because the endings show the grammatical roles.

The neutral/basic order here is:

• Moja siostra chowa dwanaście flamastrów do pudełka po lekcji.

But other orders are possible, for example:

• Po lekcji moja siostra chowa dwanaście flamastrów do pudełka.
• Dwanaście flamastrów moja siostra chowa do pudełka po lekcji.

These versions may sound more natural in different contexts depending on what you want to emphasize.

Even though the order can change, the original version is a good standard sentence for learners.

Because each word has a different grammatical job in the sentence.

• siostra is the subject, so it is in the nominative
• flamastrów is the noun after dwanaście, so it is in the genitive plural
• pudełka comes after do, so it is in the genitive
• lekcji comes after po meaning after, so it is in the locative

So the endings change because Polish uses cases to show relationships that English often shows with word order and prepositions.

Yes, the singular is natural here.

• po lekcji = after the lesson / after class

In Polish, this can also sound quite natural in a general everyday sense, similar to English after class.

If you specifically wanted after lessons or after classes in the plural, you could say:

• po lekcjach

So the difference is roughly:

• po lekcji = after class / after the lesson
• po lekcjach = after classes / after lessons

A rough English-friendly pronunciation is:

• MO-ya SHOST-ra HO-va dfa-NA-shche fla-MA-stroof do poo-DEW-ka po LEK-tsyee

A few helpful notes:

• moja sounds like MO-ya
• siostra begins with sh, so SHOST-ra
• ch in chowa sounds like a throaty h
• dwanaście is approximately dva-NA-shche
• ó in flamastrów sounds like oo
• cj in lekcji sounds roughly like ktsyi

You do not need a perfect accent immediately; the most important thing is noticing the main stress, which in Polish is usually on the second-to-last syllable.

Chować is usually imperfective.

That means it can describe:

• a repeated action
• an ongoing action
• a general action without focusing on completion

If you want a more clearly completed action, Polish often uses a perfective partner such as:

• schować

So:

• Moja siostra chowa... = My sister is putting away / puts away...
• Moja siostra schowała... = My sister put away / hid...

In your sentence, chowa is perfectly fine if the focus is simply on the action itself, not necessarily its completion.