To include an acronym or abbreviation of an organisation's full name in APA in-text references using EndNote, please follow these steps.
In EndNote, input the organisation's full name in the Author field, adding a comma after the final word.

First time the reference is used in Word:
With your cursor placed in the relevant in-text citation, go to the EndNote ribbon and choose Edit & Manage Citations.
In the Edit Citation pane at the bottom of the pop up window, click the Formatting drop down arrow for options, and select Exclude Author. Follow the instructions below depending on how you want the in-text citation to present:
(Author, Year): manually type the author's name and the acronym in square brackets in the Prefix field, remembering to type a comma and space after the second bracket. Click OK.

The citation will be:

Author (Year): having chosen Exclude Author in the Edit and Manage Citations window, only type AHRC in the Prefix field. In the Word document, manually type the author's name in full in the text before the (EndNote) in-text citation.

The citation will be (note: EndNote citation highlighted):

Subsequent in-text references using the acronym only.