Dole u dveří stojí tři krabice a jednu z nich musíme odnést do auta.

Yes, you could also say Tři krabice stojí dole u dveří.

Czech word order is fairly flexible, and it often reflects what is being set up as the topic or scene.

• Dole u dveří stojí tři krabice = first sets the location: Down by the door...
• Tři krabice stojí dole u dveří = first introduces the boxes.

Both are grammatical. The original version sounds natural because it first tells you where to look, and then tells you what is there.

Because dole expresses location, while dolů expresses movement downward.

• dole = down below / downstairs / at the bottom
• dolů = downward / down

Here the boxes are already there, so Czech uses dole:

• Dole u dveří stojí tři krabice. = The boxes are down there / downstairs / below by the door.

If someone were moving down, you would use dolů:

• Jdeme dolů. = We are going down.

The preposition u takes the genitive case, so dveře changes to dveří.

Also, dveře is one of those Czech nouns that is normally used only in the plural, even when English would say door in the singular.

So:

• dveře = door / doors
• u dveří = by the door

This is similar to how English has nouns like scissors or pants, which are grammatically plural even when they refer to one thing.

In Czech, stát is often used for things that are standing upright or simply positioned somewhere in a stable way.

So krabice stojí can sound completely normal in Czech if the boxes are upright.

• stát = stand
• ležet = lie
• viset = hang

Czech often chooses these verbs more specifically than English does. English often just says there are or are sitting. Czech prefers a more physical description.

So stojí tři krabice is not strange; it means the boxes are standing there.

Because in the present tense, 3rd person singular and 3rd person plural of stát are both stojí.

So:

• on stojí = he/it stands
• oni stojí = they stand

You know it is plural from the subject:

• tři krabice = three boxes

So here stojí must mean stand rather than stands.

Because krabice is one of those Czech nouns whose nominative singular and nominative plural have the same form.

So:

• ta krabice = the box
• ty krabice = the boxes

You tell singular vs. plural from other words in the sentence:

• jedna krabice = one box
• tři krabice = three boxes

So in your sentence, tři clearly shows that krabice is plural.

Yes — jednu is feminine accusative singular, and it refers back to krabice.

The full idea is:

• jednu (krabici) = one (box)

Czech often leaves the noun out when it is obvious from context.

Why jednu?

• jeden / jedna / jedno = one
• jednu = accusative feminine singular

It is accusative because it is the direct object of odnést:

• musíme odnést jednu z nich = we must carry away one of them

Since krabice is feminine, the form must be feminine too.

z takes the genitive, so nich here is genitive plural.

• jednu z nich = one of them

This is a very common pattern in Czech:

• jeden z nás = one of us
• jedna z těch knih = one of those books
• jednu z nich = one of them

As for nich vs. jich:

• jich is the form without a preposition
• nich is used after a preposition

So after z, you need nich, not jich.

Because muset is a modal verb, and modal verbs in Czech are followed by an infinitive.

So:

• musíme = we must / we have to
• odnést = to carry away / to take away

Together:

• musíme odnést = we must carry away

This works just like English:

• we must go
• we have to do it

Czech does the same thing:

• musíme jít
• musíme to udělat
• musíme odnést jednu z nich

Because odnést is perfective, and here the sentence talks about one complete action: taking one box away to the car.

• odnést = to carry away, as a completed act
• odnášet = to be carrying away / to carry away repeatedly or as a process

So:

• musíme odnést jednu z nich = we need to take one of them away, successfully, as a completed task

If you used odnášet, it would sound more like an ongoing or repeated activity.

This is a very common Czech pattern: after muset, Czech often uses a perfective infinitive when the goal is to complete the action.

The prefix od- adds the idea of away from a place.

Base verb:

• nést = to carry

With od-:

• odnést = to carry away / take away

So the sentence does not just mean carry a box; it means remove it from where it is and take it away, specifically to the car.

You can compare:

• nést = carry
• odnést = carry away
• přinést = bring here
• donést = carry/bring to a destination

Because do expresses motion into something, and do takes the genitive case.

• auto = car
• do auta = into the car / to the car

So:

• odnést do auta = carry it to/into the car

Compare:

• v autě = in the car — location, not motion
• do auta = into the car — motion toward the inside

The form auta is the genitive singular of auto.