Learn Hardcore Dutch: Op kantoor zit Tom de hele dag op een nieuwe bureaustoel. - At the office Tom sits all day on a new office chair.

Dutch main clauses follow the verb‑second (V2) rule: the conjugated verb must be in second position.
Here, Op kantoor (at the office) is one chunk in first position, so the finite verb zit must come next, and then comes the subject Tom.
So: Op kantoor (1st position) + zit (2nd) + Tom (3rd).
You could also start with the subject: Tom zit de hele dag op kantoor op een nieuwe bureaustoel. That is equally correct, just a different emphasis.

Why do we use zit and not is or werkt here?

Dutch often uses posture verbs like zitten (sit), staan (stand), liggen (lie), lopen (walk) instead of zijn (to be) when describing what someone is doing.
Tom zit op een bureaustoel focuses on the fact that he is sitting. In English you might say Tom is sitting or Tom sits.
Op kantoor is Tom de hele dag op een bureaustoel sounds strange in Dutch, because is doesn’t describe an activity or posture.
If you want to emphasise his job rather than his posture, you might say Op kantoor werkt Tom de hele dag (At the office, Tom works all day).

Does zit here mean “sits” or “is sitting”? How do I know which present tense to use in English?

Dutch simple present covers both English present simple and present continuous.
So Tom zit de hele dag op een nieuwe bureaustoel can be translated as either:

Tom sits on a new office chair all day. (habit)
Tom is sitting on a new office chair all day. (situation going on now)
Context decides which English tense feels more natural; the Dutch form itself does not change.

Why is there no article in op kantoor? Why not op het kantoor?

Op kantoor is a fixed, idiomatic expression meaning “at the office / at work”, in a general sense, so it normally has no article.
If you say op het kantoor, you point to one specific office building or room: at the (particular) office.
Compare:

Hij is op kantoor. – He is at the office (his workplace in general).
Hij is op het kantoor aan de overkant. – He is in the office across the street (a specific building).

What exactly does de hele dag mean, and why do we have de there when English just says “all day”?

De hele dag literally means “the whole day”, and that’s the normal way to say “all day” in Dutch.
English drops the, but Dutch keeps the definite article because dag is a common‑gender noun (de dag).
So you usually say de hele dag, not just hele dag.
In many contexts heel de dag is also possible and means the same, but de hele dag is the safest standard form.

Why is the preposition op used twice: op kantoor and op een nieuwe bureaustoel? Could you use in instead?

Dutch uses op with certain locations and surfaces:

op kantoor = at the office (as a workplace)
op een stoel zitten = to sit on a chair
If you say in het kantoor, you emphasise being inside the office room or building; that’s more spatial and less about “being at work”.
For chairs, Dutch says op een stoel zitten, not in een stoel, except for deep armchairs or sofas where you might hear in een fauteuil zitten.

Why is bureaustoel written as one word and not bureau stoel?

Dutch forms compound nouns by writing the parts together as one word.
Bureaustoel = bureau (desk/office) + stoel (chair), meaning office chair / desk chair.
In such compounds, the last part is the main noun, so the gender and plural come from stoel:

de stoel → de bureaustoel
de stoelen → de bureaustoelen
Writing it as bureau stoel would be incorrect spelling.

Why is it een nieuwe bureaustoel and not een nieuw bureaustoel?

Attributive adjectives (adjectives placed before a noun) almost always get an ‑e ending: nieuwe.
There’s one big exception: with een + singular, neuter noun, you drop the ‑e, e.g. een nieuw huis (huis = het‑word).
But stoel is a common‑gender noun (de stoel), not neuter, so the adjective keeps the ‑e:

een nieuwe stoel
de nieuwe stoel
nieuwe stoelen
Therefore we say een nieuwe bureaustoel, not een nieuw bureaustoel.

Can I leave out een and just say op nieuwe bureaustoel?

No. In Dutch, a singular countable noun almost always needs an article or another determiner.
So you need een, de, zijn, mijn, etc.:

op een nieuwe bureaustoel
op de nieuwe bureaustoel
op zijn nieuwe bureaustoel
You only drop the article if the noun is plural or uncountable, e.g. op nieuwe bureaustoelen (on new office chairs).

Can I move de hele dag or op kantoor to other positions in the sentence?

Yes, Dutch word order is quite flexible for adverbials, and you can change the focus by moving them. All of these are correct, with slightly different emphasis:

Tom zit de hele dag op kantoor op een nieuwe bureaustoel.
De hele dag zit Tom op kantoor op een nieuwe bureaustoel.
Op kantoor zit Tom de hele dag op een nieuwe bureaustoel. (original)
You can also put de hele dag at the end: Op kantoor zit Tom op een nieuwe bureaustoel de hele dag. That is possible, but the most neutral positions for de hele dag are right after the verb or right after the subject.

Is there any meaning difference between een nieuwe bureaustoel and zijn nieuwe bureaustoel?

Yes.
Een nieuwe bureaustoel = a new office chair, unspecific: we just know the chair is new, not whose it is.
Zijn nieuwe bureaustoel = his new office chair, clearly belongs to Tom (or to some “he” from context).
So Op kantoor zit Tom de hele dag op een nieuwe bureaustoel doesn’t say whether the chair is his, just that he is sitting on some new office chair.