Dokument jest głęboko w szufladzie.

A literal breakdown is:

• Dokument = document
• jest = is
• głęboko = deep / deeply
• w = in
• szufladzie = drawer in the locative case

So the whole sentence is literally The document is deep in the drawer.

Because the preposition w takes the locative case when it means in as a location.

So:

• szuflada = the basic dictionary form, nominative
• w szufladzie = in the drawer, locative

This is a very common pattern in Polish:

• w domu = in the house
• w pokoju = in the room
• w szufladzie = in the drawer

Dokument is in the nominative case, because it is the subject of the sentence.

The sentence is about the document, and Polish normally puts the subject in the nominative:

• Dokument jest... = The document is...

Because głęboko is an adverb, while głęboki is an adjective.

Here, you are not describing what kind of document it is. You are describing where it is located or how far inside the drawer it is.

• głęboki dokument would mean a deep document, which makes no sense here
• głęboko w szufladzie means deep in the drawer

So Polish uses the adverb głęboko.

It means the document is far inside the drawer, not just somewhere in it.

Depending on context, it could suggest:

• deep inside the drawer
• far back in the drawer
• buried under other things in the drawer

If you only want to say The document is in the drawer, you can simply say:

• Dokument jest w szufladzie.

Adding głęboko gives extra detail and emphasis.

In this sentence, jest is normally needed.

• Dokument jest w szufladzie. = a full, normal sentence
• Dokument w szufladzie. = more like a note, label, or incomplete phrase

Polish does sometimes avoid jest in sentences like:

• Jan to nauczyciel. = Jan is a teacher.

But with location sentences like this, jest is normally used in standard Polish.

Because w is used for location, while do is used for movement toward the inside of something.

Here the document is already inside the drawer, so Polish uses w:

• Dokument jest w szufladzie. = The document is in the drawer.

If you were talking about putting it there, you would use do:

• Wkładam dokument do szuflady. = I am putting the document into the drawer.

So:

• w = in
• do = into / to

Yes, Polish word order is fairly flexible, but the emphasis changes.

The most neutral version is:

• Dokument jest głęboko w szufladzie.

You could also say:

• Głęboko w szufladzie jest dokument.

That sounds more marked or literary, with emphasis on where it is.

English speakers should usually learn the neutral order first and use that unless they have a reason to emphasize something.

It is best understood as describing the whole location phrase w szufladzie.

So the meaning is not really the document deeply is. It is the document is deep in the drawer.

In other words, głęboko tells you how far inside the drawer the document is.

Polish does not have articles like a and the.

So Dokument can mean:

• a document
• the document

Which one is meant depends on context.

The same is true for szufladzie:

• in a drawer
• in the drawer

English requires articles, but Polish does not.

Yes, it is understandable and natural.

A simpler, more basic sentence would be:

• Dokument jest w szufladzie.

Adding głęboko makes it more specific.

In some situations, a Pole might also say:

• Dokument jest na dnie szuflady. = The document is at the bottom of the drawer.

That is a bit more specific than głęboko w szufladzie. The original sentence is still perfectly fine and natural.