Even though you kill Mannimarco, you never destoy his phylactery. Does that mean he can (and maybe will) come back later in the series?

Mannimarco is still around. Or rather, Revenant (his godform/plane(t)) is. The Jills couldn't mend his godhood, so they just dropped a mortal copy on Nirn and let it slide.

Who are the Jills again? And why would they do that?

On a side note. Is there something lore that connects the Sloads to the worship of Mannimarco?

Mortal copy? What do you mean? How does it fit in the timeline?

Mannimarco is a god (the God of Worms), I believe thanks to the Warp in the West..

the Mannimarco we face in Oblivion is but his Avatar/Aspect

But he still has a phylactery. If he was killed (NOT HIS AVATAR) would he simply reincarnate ?

Let's take this from the beginning.

Mannimarco was a powerful lich who ascended to godhood during the Warp in the West, which was a dragonbreak; a localized 'period' of time during which time itself becomes non-linear. All outcomes happen simultaneously, people give birth to their own fathers, that kinda stuff. But this can't be allowed to go on forever, so Akatosh (who is Time) has a group of female dragons known as Jills, the minute-menders, to help patch him up again when this happens.

So the Jills were doing their thing, trying to put Akatosh back as well as they could, when they stumbled upon Mannimarco's godform (most (but not all; Tribunal is one example) gods exist in the Mundus in the forms of planets or planes of existence, more commonly known as plane(t)s). Mannimarco was a god, and so the Jills could not touch him, he was outside their sphere of influence, so in their attempt to reconstruct a linear narrative of time they 1) made it so that the godform, also known as Revenant or the Necromancer's Moon, had always been a god, and 2) recreated the mortal Mannimarco. The dragonbreak ended, and now we have two Mannimarcos: the God of Worms up in the void and the King of Worms down on Nirn.

So yeah. The guy you met in Oblivion was his mortal double. You killed him (maybe), but that did nothing whatsoever to his godform, who is still up there, occasionally causing a celestial event during which Arkay's hold over the dead loosens and necromancers can circumvent Arkay's protection.

Mannimarco is variously known as the King/God of Worms and the High Priest of Maggots. Sload are sometimes referred to as "worms" or "grubs", especially in http://www.imperial-library.info/content/facing-necromancerhttp://www.imperial-library.info/content/ancient-dwemer-ruins-part-1. I had a talk about this with OPGreenback once, and he had more sources, I just can't remember them right now.

Yes. This is a pet subject of mine.

http://www.imperial-library.info/content/interviews-skeleton-man notes, following the Warp, “...that the Sload Priests talk to their new God of Worms…”

http://www.imperial-library.info/content/pocket-guide-empire-third-edition-thras notes Mannimarco (especially under his title as the King of Worms) as a hero of the Sload.

In TESA: Redguard, N'gasta and Cyrus use the word worm to refer to Sload: For example, "craftsworm". I like to take particular note of this in association with the titles King of Worms and God of Worms; worm doesn't just refer to necromancers or maggots, but to Sload as well.

N'gasta also seems to have gotten permission to lurk around Stros M'kai from Mannimarco: "Do not speak ill, mortal, of this one's liege-lord, the King of Worms, for his grace grants these shores as this one's bountiful hunting grounds."

There are a few other points that I may as well skip because they're flimsier, and probably a few other points that I missed or forgot, but you also have the big, obvious point of necromantic associations. In general, it just makes sense.

I have tons of speculation/headcanon in this direction stored away, but those don't exactly count as points of evidence, so I'll keep them behind my back until somebody asks for them.

Heheheh.

See? He's very handy like that.

Also, correct me if I'm wrong, but isn't the phylactery a temporary arrangement in any case for the interim of the lich's transformation? So once they're properly rotten and magical, they invest their soul fully back into the corpse, which is why we can perma-kill liches in the first place.

I'm suprised nobody has mentioned this yet, but in the Elder Scrolls a phylactery is only a means to becoming a lich. Once you've actually become one it just goes back to being a normal object with no magical qualities. So if Mannimarco really was killed then he would be gone, he couldn't use his phylactery to come back. http://www.uesp.net/wiki/Oblivion:The_Path_of_Transcendencetalks about it in entry 2.

EDIT: Damn, ninja'd!

Liches do not need phylacteries once they are a lich. It's during the process of being a lich that they need one.

Does the worship of Sithis have anything to do with necromancy?

I highly doubt it, Sithis worship seems to only be the bad death cult the Dark brotherhood pretend to have.

I think the Dark Brotherhood stopped pretending a long while ago.

What about those dark guardians in Fort Farragut and the Dark Brotherhood Cheydinhal Sanctuary?

just simple necromancy, doubt it has a connection to sithis.

Who does Celedaen refer to in his book (the path of transcendence ) when he says the Sovereign?

Most likely Mannimarco, the god of worms or Mannimarco, the king of worms.

I find it hard to belive the King of Worms would grant him the secret of lichdom .

Hmm maybe, maybe not, you have to remember there are possibly two Mannimarcos due to the dragon break from Daggerfall, one stayed as the king of worms and the other become the God of worms, both could be seen as the sovereign either that or the king of worms we see in Oblivion is an avatar of the God of worms.

It's possible Mannimarco began teaching the secret of lichdom in order to build up worship or an army, or just a big FU to Arkay.

VicMMIIIis somewhere:
"Liches are undead necromancers which have embraced the power of Lichdom, placing their soul in an object called a 'Phylactery', which is usually a jar or a chest. They are selfish and power-hungry, destroying all in their searches for souls to repair the Phylactery. Extremely intelligent and powerful, they are always resurrecting if their Phylactery is not crushed. Most are in control of at least a small undead army and a tomb, and are adept spellcasters. Nether Liches were weakened for a certain time by the destruction of one of their Phylacteries. Ancient Liches are old, and much more powerful."

If Celedaen is to be belived this is wrong. If this is right it would mean whoever gave him the secret of lichdom wanted him to be under his control, to be more precise, wanted to be able to get rid of him if he became a threat. This would also mean that Mannimarco isnt dead yet and even IF his phylactery was destroyed he could still repair it or make a new one or something.

Someone corect me if i'm wrong.

Where exactly did you find that Intellectus? The lich section in the UESPWiki Bestiary? Not really a credible source since anybody can write it. If only we could find the original material they used...

Wasnt Mannimarco already killed by the hand of Galerion? If so he came back. And may come back again.

It would also prove that at least some liches reincarnate at their phylcteries