(Sorry, I see I missed a reply as I was out of the office, so this may be moot, but I think before you make a decision you should view some of the training materials and perhaps join a webinar)
The files they shared with you – ending in .ens is an output style format used when formating documents. If they have changed or added reference types that is when they would need to export a Reference Type Table for you to import into your version of endnote, so it could correctly parse any specifically named record fields and reference types (traditional reference types are things like “Journal Article” “Book” “Book Section” etc.) So if thye have told you you need to change the reference types in your library, then you need them to send you an exported “reference type table” and import that, according the instructions you read. If all they really are doing is changing the order/punctuation of the bibliography output for a manuscript, then openning and saving the .ens files they sent you and using those when you are working on a paper and inserting citations - on the bibliography ribbon/menu.
I recommend you might want to view the youtube channel and get a feel for endnote. There are 7 min quick start videos and quick start resources and free webinars you can signup for (see http://endnote.com/training) You probably want to find the PC or Mac versions, as there are some subtle differences in the location of tools, tool bars, and preferences settings.
There is also a youtube channel and other resources in the training forum of this community – for example see here: