Hello, panic_rev, and welcome to the forum. When you post, it is always best to provide as much information as possible. It would really help if you listed your ingredients and the steps you took to prepare your sauce. Then, perhaps, we could steer you in the right direction.
I have simply used 2 lbs of pureed peppers, a pint (or so) of vinegar, and a tablespoon of salt, and simmered this mixture for approximately 30 minutes and that resulted in a sauce that did not separate. So there is not any need for anything special, necessarily, although some things will help.