A separation agreement is a legal contract between you and your spouse, that solidifies your mutual understanding of your rights and duties towards each other, and toward any children in the period immediately after your separation and leading up to your divorce (if a court later makes an Order, it supersedes your agreement).
Simply put, you negotiate a separation agreement by literally sitting down with your soon-to-be-ex, and trying to commit your verbal agreements and understanding to paper. This involves discussing a very broad array of issues and arrangements relating to your current family structure and lifestyle. You must both give thought to how you want the future to look, now that you will no longer be together. This is especially true if you have children together, since you will have to work together to ensure their best interests are preserved.
You may initially try to do this without the help of a lawyer, but there are many pitfalls to that approach: you may not cover all the issues, you may overlook some legislated rights and duties that you both have to each other, and you may be imprecise in your language or use incorrect legal terms. Frankly, it is always best to have the assistance of an experienced Family Law lawyer to help – it will save you time and avoid problems in the future.