Your question is far to broad, but to deal only with particle physics basics, only Quantum theory is allowed and usually a sponsor is required. The pitfalls of the current system have been raised many times by professionals, the latest being Lee Smolin in the closing chapters of The Trouble with Physics.
Details of layout etc can be found on the websites of journals, usually the 'online' journals are easier to use they allow full colour and are not so restrictive spacewise, but you must still comply with the 'accepted limits' that according to Smolin and many others; are now placing unjustifiable limits on progress.