Incorrect numbering

I am having trouble with the in text citations being numbered as per an alphabetical numbering of the referenced authors at the end of the article. So the first citation number may be eg, “3”. I want the first intext citation to be “1” and the referenced authors list to start with this first citated author. How do I swap this situation around?

So, as I understand it, you want your citations/bibliography to be listed in order of appearance and not alphabetical.  this is a setting in the output style you are using and can be adjusted there, saved to a new name and then the word document needs to have this new style applied on the endnote ribbon in word or the format bibliography in older versions of word. 

Or you can choose to use a style (like nature) which numbers them already in order of appearance, rather than the out put style you are using (which one is it?).  What journal are you targeting the manuscript to?