I use Microsoft Word, the book publishing industry standard, to edit your documents although I can also use Pages, Scrivener, Google Docs, or OpenOffice as requested.
I edit directly on screen using Track Changes, which allows changes to be tracked neatly, keeping the manuscript as clean as possible. The manuscript can also be transmitted quickly and cost effectively.
Track Changes in Microsoft Word (preferred) or Pages, or Record Changes in OpenOffice, is the most convenient method of editing a manuscript because suggestions and changes can be accepted or rejected directly within the document.
Adobe Acrobat is best used for proofreading in which the document's formatting is not compromised while comments and corrections may be easily noted.
My primary references are the Chicago Manual of Style and The Christian Writer's Manual of Style. Additionally, I refer to The Copyeditor's Handbook by Amy Einsohn.
Merriam-Webster's Collegiate Dictionary serves as my primary lexicon, and I defer to Garner's Modern American Usage on questions of semantic dispute.