How far back is the earliest known U.S usage of marking information Secret/Top Secret that still remains restricted knowledge to this day?

This is really something that can not be determined.

The classification system isn't limit to "Secrect/Top Secret", nor is it limited to just linear "you can't see that". Classification depends on the agency and the requirements there in, as well as individual clearance.

The general classification within the Department of Defense is " Unclassified, Official, Restricted, Confidential, Secret and Top Secret". However, granting of a clearance doesn't equate to an "end all, be all". A Nuke Tech on a sub holds a TS, but that doesn't clear them to view other classified material outside of their specialty, regardless of the clearance level of the material.

Additionally material may be labelled TS and falls within the Techs specialty, but may be marked "Eyes Only" or have other markings that restrict it's viewing to various parties, these are known as "caveats".

You may be an NSA employee or contractor, who's been granted Sensitive Compartmented Intelligence clearance (which is a rough equivalent to DoD Top Secret) to view all "TALENT KEYHOLE - SPECIAL INTELLIGENCE" materials, which pertains to IMINT (Imagery Intelligence), SIGINT (Signal Intelligence) and MASINT (Measurement and Signature Intelligence) within the SI control system. This doesn't grant you the ability to view materials in say, "ENDSEAL" or "STELLARWIND", even if the material is labeled additionally as "TALENT KEYHOLE - SPECIAL INTELLIGENCE". This is because you've not be cleared or read into those additional control systems, of which based on the TK-SI label contain various types of intelligence.

What makes the TK-SI clearance different than say ES-SI, is that as a TK-SI cleared individual you see the collection and analysis of the intelligence collected, but never the final dissemination or composition of the intelligence which is what ES-SI pertains to.

This is known as "compartmentalization". It allows information to be viewed by various parties within different control systems, thus allowing personnel to preform their specialties without compromising the data itself.

Additionally, with a TK-SI this does not grant the ability to view "DoD TS" or "DoE Q" classified materials, of both which are the rough equivalent to "SCI".

TS pertains to various materials within the DoD, some of which may not be intelligence, but physical materials or a particular procedure.

Department of Energy "Q clearance" pertains to Q-Nonsensitive, which grants access to TOP SECRET-Formerly Restricted Data and National Security Information materials and Q-Sensitive which grants access to TOP SECRET-Restricted Data, as well as TOP SECRET-Formerly Restricted Data and National Security Information.

An Single Scope Background Check is preformed on an individual trying to obtain a TS, SCI or Q clearance level. This is an extremely in-depth and invasion investigation. Investigators will visit family, friends, teachers, former/current employers, ect... they look into financial records, school transcripts, travel history, ect... I have a personal experience with this, both having received an background check (not an SSBI, but an NACLC) and having been listed as a reference for a person for interviewing purposes by DoD Special Investigators (for a friend who was obtaining an TS clearance), questions ranged from my friends mental faculties to his political affiliations and ideals about the US as a nation.

Of course there aren't the only agencies that use classification systems, nor is it limited to intelligence or physical materials.

The Secret Service maintains "Yankee Fire" and "Yankee White" which is clearance for working with the President and Vice President.

As far as materials go, this depends on the agency, what the laws and regulations pertaining to classified materials and national security require. Information can be labelled "UNCLASSIFIED//FOR OFFICIAL USE ONLY" and still not be viewed by the general public.