Order of Numerical References

I use the Cite While You Write feature although I don’t use instant formatting because I find it irritating having the bibliography always at the bottom of my work. I am wondering if there is a way to format Endnote so when using numerical referencing, the first reference number is always (1). I have been using Endnote for a while and everytime i create the bibliography at the end, it appears as if the order of the references is random. For example, in the bibliography obviously the first reference is number 1, however this reference doesn’t appear in my text until page 14. Apologies if I am missing something fundamental here.

I am using Endntoe x5 on mac

You are presumably using a style that sorts by alpha, rather than order of appearance.  You can edit the current style to get order of appearance or pick a style that uses that sort criteria, like Nature. 

Well I am using a plugin that uses the formats set out by my university, also in the bibliography there is no form of alpha ordering. For example, the surname of the author listed as (1) is Stuart, the surname of (2) is  Kumar and (3) is Rogerson. Also if the solution you propose will fix the issue, how does one go about implementing these changes?

Do you have refs in text boxes?

I have references in the captions for figures yes, but none that are within a text box I have added for any other reason other than captions

This is probably the problem.  Word assigns fields to text boxes first –  You want to convert them to frames,following this FAQ

See  http://endnote.com/kb/82359 for a discussion of the likely cause (citation inserted into a textbox usually associated with a figure), but view  this recent solution to the problem which is a better fix than that oulined in the first link.    

Thank you very much. This is exactly what I was looking for!!!