First ensure the manuscript is being formatted with your APA 5th output style and not some other style. Selecting it in Endnote Program does not apply to the manuscript. You need to apply it directly as the style chosen for a manuscript is somewhat random! See JasonRs posting for an image of where you can see the applied style here.
APA 5th comes “out of the box” with the 2 or 3 author specifications as & and not “and”. You could try downloading a new one from the Help>web styles finder and naming it APA5th-updated, and apply that to your manuscript. You can also check your style directly by, in Endnote, Edit>Output Styles >Edit “APA 5th” and look at the Citation settings for Author Lists. For 1 to 2 authors there should be <space>&<space> and for 3 to 100 it should be <comma>&<space>.
I didn’t realize there was that separate manuscript control. When I checked it was set to “Annotated” and not “APA 5th” - so citations not appearing as I wanted. All sorted now. Thank you, so much!