Just be sure that whatever you do makes sense and helps the writer. For instance, you might respond to student texts in HTML format, creating a version of their paper that links specific sentences, words, or passages to a comments page. That type of response makes sense even if students have submitted their papers as regular word processing documents. Make sure students recognize the purpose of interspersed comments. There are a lot of ways to provide these comments.
Most students are well-acquainted with writings up and down the margins of their papers.
You simply need to explain to your students that your comments are akin to marginal commentary that they might see on a printed paper. If you avoid or use few interspersed comments, make sure students understand why. Some teachers dislike interspersed commentary, especially the kind where bracketed comments interrupt the students' text. They may not understand why those marginal comments are missing. Some students believe that the marginalia is an indication that the teacher actually took time with the text, reading every page.