Woohoo! I literally just finished right now my masterpiece trilogy that I have worked on for what seems like, ages...
I'm a bit vexed as to where I should write 'the end'. The epilogue plays a huge role in my story so I wasn't sure whether to write it at the end of the epilogue or at the end of the main story.
How do you determine where you should write 'The End'?
Actually, I would not normally write "The End." If there is an abrupt change of POV (often the case), that can be signaled by other means.
The concept of an Epilogue is that the story is over. Whatever happens in the Epilogue, and it should be short, typically represents either an outside view, or a brief comment by one of the characters. Not always. However, a long Epilogue, which is actually a continuation of the story, is rare.
Remember the movie "American Grafitti"? After the story finished, just before the closing credits, there was a brief display of the fate of its major characters, several years later. (X married Y, Z moved to Timbuktu, W joined the Army; something like that). That was an Epilogue.
Anothor kind of Epilogue is a bookend, matching the other bookend in a Prologue. Somebody (who may or may not be a character in the story) introduces the tale in the Prologue, then tells you the subsequent reaction, after it's all over, in the Epilogue.
There are other ways of doing it. But from your description, it doesn't sound like your Epilogue is really an Epilogue. If it is non-story material (such as an explanation of the cult practices of groups involved in the story) then it should be an Appendix, or something like that.
Putting "The End" at the end is a trope that played out in early cinema and, for no reason, I can decern, children's stories (usually as a variant of "they lived happily ever after, the end.")
There is a discussion "The End" on TV Tropes (time suck warning). It comes up less often than you would imagine in books mostly because the fact that you have run out of pages is a bit of a giveaway.
Personally, I would only include it if I wanted to subvert the practice or play with it in some way. I've always wanted to end a story about fish with FIN (I love bad puns so that could be a very bad idea).
Another personal favourite of mine is to have a single blank page after the text. For me, this is the literary equivalent of fading to black. (The story is over. Go read something else.)
If putting "The End" does not seem to fit, you can always leave it out (which I would anyway). As the author, you decide which conventions you follow.
Also by not explicitly saying that it is over forever, should you want to do a new cycle with the same setting, you have left that option open.
TL;DR: Don't worry about it. Those two words are the least important ones (unless you are determined to put them in).
After the last word of the story, before any aftermatter like a glossary, author's note, list of characters, timeline, or appendix.
So yes, after the epilogue, because the epilogue is still part of the story even if it's the denouement and after the climax.
In olden days writers would type "-30-" or perhaps "###" as a centered line following the last line of the manuscript. This would be intended to show that there is no more to someone reading the manuscript (such as an editor at the publishing house to which it is being submitted), lest somehow the final pages (e.g., an epilogue) may have been misplaced. Since a work of fiction often has no contents page, that oversight could potentially occur. However, when I began my career in book publishing over 50 years ago and learned to evaluate manuscript submissions, this practice of indicating "The End" was already considered amateurish, even if the writer did it intentionally with some irony in mind. If it pleases you to make some final mark at the end of your work, go ahead, but in digital files there is little to no doubt what is the last page, from the reader's perspective.
You should write 'The End' where the end is, and nowhere else. Odds is, only you know best.
Where does the reader get the feeling of completion?
Where does the circle of events close, and the rest is only history for the fans?
Exactly where the story would be complete, if the reader stopped reading...
The end of the main story. This is where all of the other authors put theirs, even if they have an epilogue.
