Decide what the message of your allegorical novel should be. While you may have a general idea of your opinion, you need to be clear on the message you will be sending. For example, if you have strong feelings about immigration, try to focus your ideas into specific issues to address in your allegory.
Develop characters that fit classical or even mythological archetypes so that they can easily be understood. This does not mean that your characters should be superficial; rather, by using archetypal characters, you can convey more meaning to your readers.
Create some clear symbols or images that will come up again and again in the novel. Symbols are objects that stand for something other than pure function. For example, a ring stands for a bond or closeness, not just jewelry.
Choose a setting that will adequately convey the message you are trying to send. While the setting does not have to be fantastical or unrealistic, it must be easily understandable and have a clear association. For instance, an allegorical novel about unwarranted hatred and cruelty in a modern place could be set during the Spanish Inquisition or Hitler's Third Reich.
Plan a plot that has clear stages like a beginning, middle and end. Give your characters something to do or seek. Make sure there is a conflict that your characters can fight to resolve. A popular allegorical device is a quest, in which the classical character is looking for something like a fountain of youth or city of gold. Outline major happenings and plot points however you see fit. Make notes that will guide you as you begin to write.