The format of the name display in your bibliography and in-text citations is dictated by rule of the Bibliographic Formatting style [aka Output Style or Style] - these can be set and modified in EndNote and in the CWYW component in MS Word. APA 5th and 6th formats usually display last name and first initial as one example.
As for entering names into your EndNote library, it is better to be consistent and use one format - Last name, first name - is usually best. Most of the time EndNote is smart enough to tell the difference when some names are entered Last name, first name and other First name, last - but not always. By entering things consistently you will make EndNote’s job easier and be happier with the results.