I'll have to do some digging to find the links to the pdf files I have, but they are mostly the reports given to USN interrogators by IJN officers post-war. There are also some after-action patrol reports from the US subs (different site) as to how they conducted their attacks. Early in the war, for some reason, the submerged sonar attack was the 'preferred' methodology, but that was quickly thrown away by most good skippers after encountering probably a 100% failure rate. Other than directives for being submerged during daylight hours early in the war (no radar), or using the magnetic pistols, it appears to me that US sub skippers had autonomy for conducting their attacks, so long as they got results. Local conditions and the ratio of the copper / zinc alloy content in the skipper's 'spheres' probably influenced whether the boat would be on the surface or submerged...
