If your not using any acid, lime, lemon juice or vinegar, then your going to want to use it quickly and refrigerate what you dont use. If you add enough acid to get the Ph. down below 4 then you'll have something that will last longer and if bottled correctly can even sit on the shelf for awhile. Read through the Making Hot Sauce thread pinned at the top for more information.
Also...if you add the chiles early, and reduce for an extended amount of time...you render the pure capsaicin oils out, and end up with a somewhat metallic, extract flavor in the sauce. When I make a sauce, I add the chiles toward the end.