What do I enter on the second K-1 I am told to file if my Form 1065 reports a number in box 2?

In theory, you should split the values in all the other boxes to reflect the amount that was associated with the rental activity of the business, and the amount that was associated with the "ordinary" business.

In practice, given that the rental activity was a very small share of the income, and assuming you have no information to make a split, frequent advice has been to simply put the values for everything except box 2 on the "ordinary" K-1, and just put box 2 on the second.  Alternatively, you could split everything proportionally.

You will need to enter each income (loss) separately as if you received 2 separate K-1's.  Generally, you will enter the business portion (Box 1) first, entering the Partnership name, ID, etc., and the income or loss amounts as if those are the only items on the K-1.  Once that data is entered, you will need to add a new K-1 for the rental loss.  As you progress through the questions, the screen asking if multiple boxes are checked will appear and should look like below:

Once you have entered the business portion of the K-1 data, you will return to the summary page where you will add another K-1 as shown below:

Enter the real estate data to the additional K-1 as if you received 2 K-1's instead of the single, composite K-1.  After all data is entered, I suggest clicking on "Edit" for each to verify that you accurately entered the data that shows on the K-1 in each of the now separate K-1's.

@terribleivan