Marking up a document in a clear way is a sign of a good copy editor or proofreader. It’s not just about using standard proofreading symbols, at least with marketing copy and when the copy is in layout. (In my markups, I avoid using some of the traditional symbols that seem old fashioned and not understandable by anyone who isn’t a typesetter.)
Any written instructions should be brief but clear. Visual elements, like arrows, boxes and circles can help clarify your instructions, as long as they aren’t redundant to the instructions. These are small techniques, but important ones.
And of course, your handwriting must be legible and in print form, never cursive. For text that you want inserted into the layout, print in the exact casing you want it to be in in the layout.
Your markup will be read by the person who will implement your changes. You should make it as clear and as easy as possible for that person to understand.
I once saw a markup a proofreader did in which many words and phrases needed to be moved to different places all over the one-page design. The proofreader had drawn so many arrowed lines connected to circled text that the page became a complicated map of crossing red lines—However, the markup was carefully done and incredibly legible!—And the production artist successfully implemented those instructions. Not an ideal situation, but a markup well done, a proofreader’s work of art.