So as a side villain in a campaign I'm doing I'm thinking about adding this villain Seth, he's a level 20 rouge mastermind, he is impossible to track, constantly he appears and confuses the party, he has no quarl with them, and does for his own amusement, however he also helps the party and secretly is manipulating them, how should I make a villain like this.

First, I'd recommend toning his level back unless the party is already 12+.  Give the villain some room to grow, if he's level 20... what does he really need?  Why especially would he need the party?

You haven't mentioned anything else about the world you're in, so I can't comment about specifics...  but continue to think on what "Moriarty" here wants?  Motivation is going to be everything.

Does he want Power?  He's level 20, he has it. 
Does he want Money? He's level 20 can steal it, hell he can convince someone to GIVE it to him.
What does a man who has everything want?  What does a man who can get anything, unable to get?  What is it a high level character can't get? 

Sure, he could be and Elf and it's been 600 years and he's bored, but that's going to feel hollow as a plot twist.

Now if he's powerful, but not omnipowerful yet, what could he be after to become omnipowerful?  Is there a Holy Grail to make him immortal?  Does he want to become a demigod of deceit?  Is there an artifact he's after, something he can't get on his own.  Could he get it on his own, but there is too much risk.
Heck the Clone spell can make ANYONE immortal, for the low cost of 3,000 gold and a cubic inch of flesh.

Maybe he's trying to get a group of Adventurer's to get it this McGuffin for him.  Will he steal it from them afterwards, or pull there strings so they willingly give it to the Big Bad?
Maybe he needs some fall guys to set things in motion.

Is he the Royal Spy Master, but also fermenting a rebellion against the king?

Is he letting information slip so the orcs can attack weapon caches and they start raiding the area?  So he can find a group to gain experience and fame?

Thanks for the ideas the one I'm disagreeing with thought is level toning, at most I'd go down to level 17 since my party has a paladin with spells that tell him if someone's lying so, on top of that he's a side villian, the main enemy of this world a plague transforming creatures into beings of darkness, the main villain is the one causing all this.

I think you're overestimating the ability to detect lies, hun.   All the rogue needs to do is not be inside the Zone of Truth spell and he's completely unaffected - that's easy to get out of unless tied down or imprisoned in some way.   Or give this Seth a magic item that grants Charisma save proficiency or advantage on the save.  Or say that he's under a Mind Blank spell.  High level just for this save is unnecessary.  

I do have to agree with FMB - why is he bothering the party?  Is this a rival thing?  If so, then Xanathar's actually has some good ideas in the Downtime section on rivals to the PCs that's worth checking out.

But having a high level NPC show up to just troll the PCs can potentially lead to annoyance, especially if the NPC is so much stronger than them and only taunts them.  I would feel like that's kind of just a GM Mary Sue character to show off, and that's just annoying without a compelling story reason for this character to do the things they do.

I guess the best advice is really to make this a fully fleshed out character above all else, with ties, emotions, drives, ambitions, flaws, bonds, organizations and more.

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I think you're overestimating the ability to detect lies, hun.   All the rogue needs to do is not be inside the Zone of Truth spell and he's completely unaffected - that's easy to get out of unless tied down or imprisoned in some way.   Or give this Seth a magic item that grants Charisma save proficiency or advantage on the save.  Or say that he's under a Mind Blank spell.  High level just for this save is unnecessary.  

I do have to agree with FMB - why is he bothering the party?  Is this a rival thing?  If so, then Xanathar's actually has some good ideas in the Downtime section on rivals to the PCs that's worth checking out.

But having a high level NPC show up to just troll the PCs can potentially lead to annoyance, especially if the NPC is so much stronger than them and only taunts them.  I would feel like that's kind of just a GM Mary Sue character to show off, and that's just annoying without a compelling story reason for this character to do the things they do.

I guess the best advice is really to make this a fully fleshed out character above all else, with ties, emotions, drives, ambitions, flaws, bonds, organizations and more.