Following Causeview's article on configuring the Enhanced Gift Batch Interface, the first two sections look like it will only make changes specific to one type of User Profile (System Administrator, for example). However when you start making changes to the Payment object (in App Setup->Create->Objects) as referenced in the third and final section of the article will this affect all of the other Users, even if they are using other types of User Profiles? Right now, we'd like to test the Enhanced Gift Batch Interface with only one type of User Profile before we extend it to our other Users.
Yes, the succeeding sections (Payment Object and Gift Batch Object) will affect all user profiles. However, on the Payment Object, you are only configuring field sets related to the creation of Gift Batch Templates (which are only used with Enhanced Gift Batch and will not affect anything else). As for the Payment Types, it is just ensuring that the methods of payment available are in-line with what is recommended in Causeview as a general rule and will actually help to keep all methods of Gift Entry consistent.
As for the Gift Batch Object, adding the Template Name field on the page layout will not prevent your users from using the former Gift Batch interface. The field is not mandatory and can be left blank.