Radije ću ostati s njom nego ići u grad.

Radije means rather or more willingly. In this sentence, it shows a preference between two actions:

• ostati s njom = stay with her
• ići u grad = go into town / go to the city

So radije ... nego ... means rather ... than ....

Croatian often uses the future tense to express a decision or preference about what someone will do:

• Radije ću ostati...
  literally: I will rather stay...
  natural English: I’d rather stay...

So even though the Croatian form is future, the most natural English translation is often would rather.

Ću is a clitic, an unstressed short word. In Croatian, clitics usually go in the second position of the clause.

So in:

• Radije ću ostati s njom...

the first element is radije, and ću comes right after it.

You could also say:

• Ja ću radije ostati s njom...

There, ja is the first element, and ću still comes very early, in the normal clitic position.

Croatian often leaves out subject pronouns when they are already clear from the verb form.

Here, ću already tells you the subject is I:

• ću = I will

So ja is not necessary unless you want extra emphasis, contrast, or clarity.

The preposition s meaning with takes the instrumental case.

The pronoun ona changes like this:

• ona = she
• nju = her
• njom = with her / by her / using her, depending on context

So:

• s njom = with her

That is why it is njom, not ona or nju.

Both s and sa are forms of the same preposition, but sa is mainly used where pronunciation is easier that way, especially before certain consonants.

With njom, the normal form is:

• s njom

So s njom is the standard choice here.

Nego means than when comparing two actions, choices, or clauses.

In this pattern:

• radije ... nego ... = rather ... than ...

So:

• Radije ću ostati s njom nego ići u grad.
• I’d rather stay with her than go into town.

A useful comparison:

• veći od mene = bigger than me
  (od is used in simple comparisons of nouns/adjectives)
• radije ostati nego ići = rather stay than go
  (nego is used to compare actions)

After nego, Croatian often uses the infinitive when comparing two actions with the same subject.

So:

• radije ću ostati ... nego ići ...

is a natural structure meaning:

• I’d rather stay ... than go ...

The second ću is not repeated because it is understood from the first part.

So the sentence is basically:

• I will rather stay than go

not:

• I will rather stay than I go

Yes, that kind of structure exists in Croatian, and you may hear things like:

• Radije ću ostati s njom nego da idem u grad.

But in your sentence, the infinitive version:

• nego ići u grad

is shorter and very natural. It is especially common when the same person is doing both actions.

Because Croatian uses different cases depending on whether you mean movement or location.

• u grad = into town / to town → direction, movement
• u gradu = in town / in the city → location

Since ići means to go, the sentence needs the form that shows movement:

• ići u grad

It can mean either, depending on context.

In everyday Croatian, ići u grad often means something like:

• go into town
• go downtown
• go to the city centre

So even though grad literally means city/town, the phrase can be a general everyday expression for going out into town.

Yes, Croatian word order is fairly flexible, but not completely free.

The sentence you have is a very natural neutral version:

• Radije ću ostati s njom nego ići u grad.

Other versions are possible for emphasis, for example:

• S njom ću radije ostati nego ići u grad.

But the clitic ću still has to stay in its normal early position. So while emphasis can shift, the basic grammar stays the same.