A sentence with listing items: How to remove the ambiguity?

Question

There is a store which trades oranges and 3 kinds of apples. And there is a person there to whom I'm giving directions. Which sentence will be the best in such a case?

• Put green apples in the first box. Put red and yellow apples and oranges in the second box.
• Put green apples in the first box. Put red and yellow apples, and oranges, in the second box.
• Put green apples in the first box. Put red and yellow apples, and also oranges, in the second box.
• Put green apples in the first box. Put red and yellow apples, as well as oranges, in the second box.

The 1st sentence looks wrong to me. We don't have red or yellow oranges.

The 2nd sentence looks OK to me, but I'm not sure that commas are enough to remove the ambiguity.

The 3rd and 4th sentences look somewhat wordy.

Edit: It is assumed that I cannot place oranges at the first place.

Answer 1

One way to reduce the ambiguity is to include articles: 

Put the green apples in the first box.  Put the red and yellow apples and the oranges in the second box.

With the definite articles in place, we can see that red and yellow applies only to apples and not to oranges.  This "red and yellow" is inside the phrase "the red and yellow apples", so it doesn't apply to the phrase "the oranges".

Using the definite article does imply that the apples and oranges in question are specified by something in the surrounding context.  That works in this context, since we're only talking about apples and oranges that are associated with the store.  In some other context, we might have reason to include unknown apples and oranges, or even hypothetical pieces of fruit.  If so, we might use a determiner like "any" or "all" to mark the same noun-phrase boundaries.

Using some determiner like the definite article could also resolve the ambiguity in the other direction:

... the red and yellow apples and oranges ...

In this example, we know that both colors apply to both kinds of fruit. 

Answer 2

Simply repeat the use of apples. Rather than using the shortcut of red and yellow apples, use the expanded form of red apples and yellow apples:

Put green apples in the first box. Put red apples, yellow apples, and oranges in the second box.

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Alternatively, given that only 4 type of things are under consideration, there is an even simpler method of approaching a concise and clearly understood set of instructions:

Put green apples in the first box. Put everything else in the second box.

Once mention is made of green apples, there is no need to enumerate the remaining items at all.

Answer 3

Another approach would be to put oranges first:

Put green apples in the first box. Put oranges and red and yellow apples in the second box.

Or if there are only green, red, and yellow apples, then:

Put green apples in the first box. Put oranges and the rest of the apples in the second box.

(or "the other apples")

Answer 4

You have two good answers. I look at this question as probably one where clarity is at premium even at the cost of inelegant language. For instance, you are giving precise packing instructions and don't want any ambiguity. If this be the case, I would make boxes central to the communication, phrasing it as:

The first box is only for green apples. In the second box, put apples ( both red and yellow) and oranges

Answer 5

Put green apples in the first box. Put red apples, yellow apples, and oranges in the second box.

Note that there is no comma after "oranges".