You make the changes directly to the object. When you publish those changes, SSDT will figure out what needs to change and make the changes directly.
I've got a bunch of posts on SSDT that might be helpful and learned quite a bit from Jamie Thomson's post on DB Projects and SSDT over the years.
http://schottsql.blogspot.com/2013/10/all-ssdt-articles.html - will work, but takes a while to build the list sometimes.
http://schottsql.blogspot.com/feeds/posts/summary/-/SSDT - definitely works, but order is most recent to oldest.