This is what I need... is there an Adobe product that is well suited for me?

My task is to open existing pdf's (usually the source is a scanned document or a converted word doc) label parts of the document with numbers and somehow indicated the paragraph of text each number applies to.  I need these "labels and mark-ups" to be saved with the pdf and also visible when the pdf is printed.  I currently use adobe acrobat commenting tools ( text box and line drawing tool) to do this.  However I am wondering if another product exist that would have different features that allow me to produce a document that looks more professional.  I do not need to edit text, just need to add labels and symbols that would allow the content to be referenced quickly.

Thanks for taking the time to read this.  It's raining where I'm at, hope your day is sunny.