If you don't have time to respond to the whole paper, mark a representative sample. Some instructors mark sentence-level problems in one or two paragraphs, then draw a line to indicate that they will respond only to content after that point. It is often best to respond as a reader, not as a critic. As you read the text, if you lose the train of thought or are confused, simply say so. Even if you can puzzle out what the writer means, the initial confusion indicates that there is a rhetorical or stylistic problem that the writer should deal with.
First impressions are often the best guide to what the major problems are.
The problems that jump out from the text are usually the ones to deal with first. The problems that appear after careful analysis are probably more subtle, more difficult to remedy, and of less immediate importance. Going with your first impression also speeds up the process of responding to writing. If at all possible arrange to have a brief conference with the student. In preparing for the conference you can mark the paper for yourself, making notes about the things you want to discuss with the student.