Eeehhhnnn, IF Superman were given a handicap- by which I mean, if he knew everything there was to know about Doctor Manhattan, and Doctor Manhattan knew nothing about Superman- then he might be able to find a way to win, even if that way consists of 'Use tachyons to fiddle with his time sense, then send him to the Phantom Zone.' (And we're going with the assumption that Doctor Manhattan wouldn't be capable of finding a way out of that realm/that the particles that he is composed of (or will that binds them) CAN be zapped there)
If Doctor Manhattan and Superman both knew all there was to know about each other, got to give it to Doctor Manhattan; teleport Superman into the middle of a red sun. Boom. Now, Superman HAS been able to pull through getting knocked through a red sun (in a battle with Superboy Prime,) but even if he DID get out of it without losing all his powers and being incinerated, Manhattan could just do it again and again til he can't get out. =P The only weaknesses Manhattan himself possesses have to do with slowing him down/ tricking him, as nobody's actually been able to slow him down for longer than a few minutes, let alone beat him outright.
If they BOTH went in blind, unaware of the others' abilities or weaknesses beforehand, I would either have to call it a stalemate, or a win for Manhattan, depending on the circumstances. First, Superman's usual go-to strategy (punch it really, really hard) isn't likely to work. Manhattan's brought himself back from disintegration, (even though an intrinsic field is fictional, it's usually thought to represent the various forces that holds matter together) so I don't see any level of strength or heat vision actually taking him down for good. Heck, Manhattan can exist as simultaneous copies sharing one consciousness, so even if he were vulnerable to harm, he could just keep splitting off copies.
Second, as he explained it in the film at least (can't remember if the comic syncs up) he is able to see his own personal timeline; any battle with Superman would fall under that perception. The only way to block it would be the same way it was done in the story, but that would require Superman having foreknowledge of Manhattan, which he wouldn't in this scenario. So, just like that, Manhattan's seen every move Superman would make against him, and presumably could change whatever outcome might normally occur. (At least, he seems to think he can, as despite supposed evidence of a nuclear war he was still working to try and develop the power source that would prevent it. Whether he CAN change the future, especially given he's described it more as there being no future, past or present, who knows.) Still, as he also said, he isn't omniscient, so even if he saw every move Superman would make in a fight, he wouldn't automatically know about Superman's weaknesses unless some idiot yelled out 'SUPERMAN TRY TO MAKE SURE HE DOESN"T LEARN ABOUT KRYPTONITE!"
Which brings us down to raw power, i.e. which can output the most 'oomph' which is the reason for the possible tie. The problem there is I'm not sure how Manhattan's more destructive abilities WORK. Superman can legitimately take a ridiculous amount of punishment, and so raw 'boom' might not be enough to beat him, or kill him; keeping in mind that Manhattan, as far as I know, mostly used his power on squishy humans (and a tank,) neither of which would be a good indicator as to his limits. And it's entirely possible that Manhattan HAS no real limits in terms of how much power he can put out, (in which case he could teleport Superman in the middle of nowhere space, and hit him with a gigantic death boom,) but it's pretty hard to say. Because of that uncertainty, I'd go with the tie, since even if Manhattan doesn't have enough raw power to beat Superman, Superman pretty much can't touch what Manhattan is, let alone hurt him. =P
As a side note, if Manhattan can, using his own abilities, reproduce the same intrinsic field subtraction, (which presumably causes all the atoms in a structure to lose cohesion) that initially killed him, then Superman would probably be no more resistant to it than anyone else. Hooooowever, while being killed by the instrinsic field subtrator is no GUARANTEE of developing superpowers- Manhattan being a special case- there's still an outside chance Superman (though, honestly, more likely Batman) could pull it off.
Zanten, Doer Of The Things
Unless He Forgets In Which Case Zanten, Forgetter Of The Things
Or He Procrascinates, In Which Case Zanten, Doer Of The Things Later
Or It Involves Moving Furniture, in Which Case Zanten, F*** You.