Before putting pen to paper (or finger to keyboard) it will make your job much easier to have an idea in mind of exactly how your paper is going to be framed.
If you're writing on a pre-assigned topic, its nature will likely affect the way in which your paper is structured.
If you're asked to "discuss" or "analyze" something (for example, "Discuss the effects of the Enlightenment on the French Revolution), it means you need to treat a specific aspect of a broad topic. It is important, in these cases, to stick to the specific focus of the prompt: don't talk about the Enlightenment itself or other aspects of the French Revolution. You must confine your paper solely to the specific relationship between the two.
When thinking about your structure, then, it's best to come up with the general areas you'd like to discuss (this will largely be determined by the amount of space you have), and to divide your paper mentally between those.
Very often you'll be asked to "compare and contrast" two pieces of literature, and there are several ways in which to effectively set up this sort of essay.
The first thing to remember (which will be explored more extensively in the thesis section) is that your paper cannot just compare the two pieces in general, exhaustively mentioning all similarities and differences with no specific argument.
Once you know exactly what your argument is, your structure will be crucial to the techniques you use to make it.
The sequential method - This means discussing all of text A and then moving on to text B.
Example: The prompt says "Compare Milton's view of Hell in "Paradise Lost" with that of Marlowe in "Dr. Faustus." It might be easier, here, to spend your first pages thoroughly analyzing Milton's view and then moving on to Marlowe's independently. It is then key, however, that your conclusion be a successful integration off he two or else you won't have a unifying argument.
The point-by-point method - This method works well if you have a number of parallel specifics to deal with in both texts, and involves discussing each one in turn, with respect to both texts at once.
Example: The prompt says "Discuss the relationship between symbolism and character in Faulkner's Light in August and Steinbeck's The Grapes of Wrath." In this case, it might be easier to discuss the individual relationships one at time. You could discuss Christ imagery in both texts first, for example, and move on to erotic symbols and so forth.
This type of comparative paper concentrates on one particular text, but views it through the "lens" of another.
Example: Discuss "The Rape of the Lock" in terms of mock epic, with reference to Homer's The Illiad.
In this case, the second text should be used as a continual reference point, but should not be analyzed in and of itself.
A way to structure this sort of paper is to break down your argument with respect to your main text into a number of points, as you normally would with a "discuss" paper. Within each paragraph, insert segments of analysis as to how your new arguments function within the paradigms established by the lens text.