Have more than one villain - and develop all of your villains into full characters who, besides their "villaining" dark side, have neutral and good traits as well.
Go for realism character-wise. Nobody's entirely good or evil. Every power player has some good in them (and they might turn out to be the father of one of your PCs as well. Especially if the PC is called Luke. :))
In the case of the "friendly" villain, whose agenda you wish the PCs to further, focus on the positive traits. Illustrate them regularly, but not always by casting direct light on them (that would be too obvious), but subtly, through hints and clues, and contrast them with the negative traits of the "enemy".
Example: When a PC gets shot by a rival mobster, he's taken to a hospital for a few days, where he accidentally overhears a conversation between a woman and a doctor. Turns out she's the wife of your friendly don Villainetti, and she's interviewing the doctor about the needs of the hospital, for she and her husband are about to donate a larger sum to the institution which saved their daughter's life. The doctor (a top member of the hospital's board) doesn't want to accept the donation, for he's afraid the cops, lead by Chief Inspector Goodman, a pawn of Mayor Major, would use it - their accepting Villainetti's money, that is - in the political game to oust the current board of the hospital and fill the positions with their medically incompetent lackeys. Villainetti's wife responds to this that she and her husband know this, and are willing to donate anonymously - which shows that they really are thankful. So, who's evil here? Sure everyone, a bit. For when the PC recovers, he and the party gets asked by Villainetti to arrange some money laundering for him. For the hospital, of course. Only for the hospital. Problem is, CI Goodman has too many eyes. Some should be forced shut for a while.
Yes, the above example would partially fit the third point of @WhiteWolfDM's answer (a good one that I upvoted) as well. What I'm trying to emphasize here, in contrast with that, is that there should be real good in your friendly villain, that he should be a layered, well developed character, more dark gray than black... and that his enemies, against whom he's going to use the PCs, shouldn't really be simple victims either, most of the time: they should be just as fully rounded, gray figures. A cop - who beats his wife (who's slowly poisoning him in turn.) A state prosecutor - who sent her husband to jail using fabricated, false evidence to get rid of him (because he's been cheating on her, in turn, because..., because...)
You get the idea, I guess. Complex layers of opposing personalities, contradictory layers of information, slow revelations. :)
But, as @valadil said in a comment: Be careful, don't overdo it. You don't want frustrated players turning away from your storytelling. Give them successes.