Puer lapidem e via tollit et in cista ponit.

Puer is the subject because it is in the nominative singular, the case normally used for the doer of the action.

The ending may look surprising if you are expecting second-declension masculine nouns to end in -us, but some of them end in -er instead.
So:

• puer = boy
• dictionary form: puer, pueri

It is still a regular second-declension noun; it just belongs to the -er type.

Because lapidem is the accusative singular, used for the direct object.

Here, the boy is doing something to the stone, so stone must be in the accusative:

• nominative: lapis = stone
• accusative: lapidem = stone as the thing affected by the verb

This noun is third declension:

• lapis, lapidis

So the sentence shows:

• puer = the doer
• lapidem = the thing being picked up and put somewhere

The preposition e (or ex) means out of, from and it takes the ablative case.

So in e via:

• e = from / out of
• via = road, street, path
• with a macron, the ablative form is viā

Many beginner texts leave macrons out, so you see via instead of viā.

Both e and ex mean the same thing: from / out of.

A common pattern is:

• e before a consonant
• ex before a vowel or h

Since via begins with the consonant sound v, e via is perfectly natural.

That said, Latin usage is not completely rigid, and you will sometimes see variation.

Because the difference is often shown only by macrons, and many Latin texts omit them.

For first-declension nouns:

• nominative singular: -a
• ablative singular: -ā

So:

• via can be nominative via
• viā is ablative, but without the macron it is also written via
• cista
• cistā likewise becomes cista if the macron is omitted

You know the case from the grammar:

• e takes the ablative
• in here also uses the ablative

This is a very common learner question.

The basic rule is:

• in + accusative = into
• in + ablative = in / on

So a beginner may expect in cistam for into the box.

However, with verbs of placing such as pono (put, place), Latin can also use in + ablative to show the place where something is placed, with attention on the resulting location.

So:

• in cista = in the box, focusing on where the stone ends up
• in cistam would emphasize movement into the box more strongly

In this sentence, Latin uses in cista. With macrons, that would be in cistā.

Because Latin has no articles.

So a noun like puer can mean:

• the boy
• a boy

And lapidem can mean:

• the stone
• a stone

Which one is meant depends on context. English must choose; Latin usually does not.

Latin often leaves out words that are already clear from context.

In et in cista ponit:

• the subject is still puer
• the thing being put is still lapidem

Latin does not need to repeat them because the meaning is obvious.

Also, the verb ending -t in ponit already tells you the subject is he/she/it. In context, that means the boy.

Tollit is 3rd person singular present active indicative of tollo, tollere.

So it means:

• he lifts
• he picks up
• he removes

In this sentence, because of e via, the idea is something like he picks the stone up from the road or he removes the stone from the road.

Ponit is 3rd person singular present active indicative of pono, ponere.

It means:

• he puts
• he places

So the two verbs match neatly:

• tollit = he picks up
• ponit = he puts

Both are in the present tense, and both have the same understood subject: the boy.

Latin word order is much more flexible than English word order because Latin uses case endings to show each word’s role.

English depends heavily on position:

• The boy picks up the stone

Latin can move words around more freely because:

• puer is nominative
• lapidem is accusative

So even if the order changes, the grammar still tells you who is doing what.

This sentence has a very natural Latin feel:

• Puer lapidem e via tollit et in cista ponit.

It is not the only possible order, but it is clear and idiomatic. Latin often likes to place the verb toward the end of the clause.