Arı çiçeklerin üstünde dolaşıyor, kelebek ise daha yukarıda uçuyor.

The Turkish ı is the dotless i, and it does not sound like English ee.

A rough guide:

• arı sounds something like uh-RUH (very approximate)
• dolaşıyor has the same vowel in şı

The sound is a relaxed, back vowel. English does not have an exact match, so it takes practice. The important thing is:

• i = like ee in see
• ı = a different sound, with no dot

So arı and dolaşıyor should not be pronounced with the normal English ee sound.

Because çiçeklerin is made of:

• çiçek = flower
• -ler = plural
• -in = genitive ending, meaning of the

So:

• çiçekler = flowers
• çiçeklerin = of the flowers / the flowers'

This genitive form is needed because Turkish often uses a structure like:

• X-in üstünde = on top of X / above X
• X-in altında = under X
• X-in önünde = in front of X

Üstünde breaks down like this:

• üst = top, upper side
• üstü = its top / the top of it
• üstünde = on its top / on top of it / over it

So:

• çiçeklerin üstünde literally means something like on the flowers' upper side or over the flowers
• in natural English, this becomes over the flowers or above the flowers

This is a very common Turkish pattern with location words:

• masanın üstünde = on the table
• evin önünde = in front of the house
• sandalyenin arkasında = behind the chair

Because the meanings are different.

• çiçeklerin üstünde = over/on top of the flowers
• çiçeklerde = in/on the flowers or at the flowers, depending on context

Here the sentence is describing where the bee is moving in space, so üstünde is more precise. It suggests the bee is flying or moving around above the flowers, not simply located in or on them.

Dolaşıyor comes from dolaşmak, which means things like:

• to wander
• to move around
• to roam
• to go around

In this sentence, for a bee, it suggests:

• buzzing around
• moving around over the flowers
• going from place to place around them

So it is more than just uçuyor (is flying). It gives the idea of circling around / hovering around / moving about, not just the basic fact of flight.

Because the two verbs give different pictures.

• dolaşıyor = moving around, wandering, hovering about
• uçuyor = flying

So the sentence contrasts two kinds of movement:

• the bee is moving around over the flowers
• the butterfly is flying higher up

Using different verbs makes the scene more vivid and natural.

Here, ise does not mean if.

In this sentence, ise works as a contrast marker. It means something like:

• as for
• while
• whereas
• however

So:

• kelebek ise = as for the butterfly / the butterfly, however

It helps set up a contrast between the bee and the butterfly.

Without ise, the sentence would still be grammatical, but the contrast would be weaker.

Daha means more or marks a comparison.

So:

• yukarıda = up / above / higher up
• daha yukarıda = higher up / further up

The comparison is understood from the first clause:

• the bee is over the flowers
• the butterfly is higher than that

Turkish often leaves the comparison target unstated when it is obvious from context.

• yukarı = up, upward, upstairs, above
• yukarıda = up there, above, in a higher place

The -da ending is the locative ending, meaning in / at / on a place.

So in this sentence:

• daha yukarıda uçuyor = is flying higher up / is flying in a higher position

If you removed -da, the phrase would not work the same way here. The sentence needs the location form.

They are in the present continuous tense, formed with -yor.

• dolaşıyor = is moving around / is wandering
• uçuyor = is flying

This tense is very common in Turkish for actions happening right now or for describing a scene in progress.

Here it matches English is ...-ing very well.

The given word order is natural and neutral, but Turkish word order is fairly flexible.

This sentence is arranged as:

• Arı = topic/subject
• çiçeklerin üstünde = location
• dolaşıyor = verb

and then:

• kelebek ise = contrasting topic
• daha yukarıda = location
• uçuyor = verb

Putting the verb at the end is the most standard Turkish pattern.
You can move other parts around for emphasis, but that changes the focus and tone.

So this version is a very natural way to present the scene.

Yes, üzerinde is also possible in many contexts.

• üstünde
• üzerinde

Both can mean on, over, or on top of, depending on context.

Very roughly:

• üstünde can feel a bit more concrete or spatial: on top / over
• üzerinde can sound a bit more neutral or formal in some contexts

In this sentence, çiçeklerin üstünde is completely natural.
A learner should understand both, because both are very common in Turkish.