The United States Code consists of the federal statutes that are (a) general, (b) permanent, and © codified. The codification consists of 50 “titles” into which (theoretically) all the general and permanent statutes have been organized. Titles 1 through 6 are basic provisions organizing the nation and its major institutions; titles 7 through 50 are organized alphabetically by topic, from Agriculture (title 7) to War and National Defense (title 50).
An appendix is just what it sounds like: material appended to a title that is closely related to its subject matter, but does not belong within the code itself. Ten titles have an appendix. The appendix to title 50, War and National Defense, which the OP asked about, consists of a collection of PROCLAMATIONS, EXECUTIVE ORDERS, JOINT RESOLUTIONS AND TREATIES RESPECTING WAR, NEUTRALITY AND PEACE, followed by more than 80 statutes that relate to war and national defense but which haven’t made it into the code.
Some material goes into an appendix rather than the code itself because it is not statutory. For example, the title that I consult most often is title 28, Judiciary and Judicial Procedure, whose appendix contains various court rules–including the Federal Rules of Civil Procedure, the Fedral Rules of Evidence, the Federal Rules of Appellate Procedure, and the Rules of the Supreme Court of the United States, among others. Likewise, title 18, Crimes and Criminal Procedure, has an appendix that contains the Federal Rules of Criminal Procedure. Title 10, Armed Forces, has an appendix that contains the Rules of Practice and Procedure for the United States Court of Appeals for the Armed Forces. Title 26, the Internal Revenue Code, has an appendix that contains the rules for the Tax Court. These rules are not statutes enacted by the Congress, but rules adopted by the various federal courts for practice and procedure before them, which have the force of law.
Some appendices contain statutes that have been enacted into law but not codified. The process of codifying all the general and permanent laws into a single topically-arranged code has been going on for decades, and will continue for decades more; most titles have been acted into positive law, meaning that the codified title itself is the law and the stand-alone statutes that have been compiled into it have been merged into the code, but nearly half the titles are simply the revisor’s proposed arrangement which is awaiting congressional action. Meanwhile, Congress keeps legislating in new subject areas, and those statutes stand alone until they can be codified into the existing numerical scheme, sometimes many years or decades later. (The codification process gets around to roughly one title per Congress.) If a stand-alone statute clearly relates to an existing title, but does not fit into the title’s existing structure, it is appended to the title for convenient reference until the codification process gets around (or back around) to it.