Darth Plagueis the Wise, could alter the midichlorians to "create life".
His "student" learned all his secrets before he "killed" him in his sleep.
Anikin had no father, Shmi "could not explain it".
Sidious KNEW of the prophecy of the "chosen one" who would bring order. Even if the Jedi had successfully hidden the story, in the past, Sidious could have heard it from Duku, who would have known all about it.
The same way he planned to have the clone army ready in advance.
The same way he had the droid army attack his own planet.
He, or his master Plagueis, could have altered Shmi's body to cause her to have Anikin, And WAITED for him to mature. THere could possibly even be OTHERS, in case of a freak podracing accident or something.
Anikin was then dropped in front of them on purpose.
Sidious and Vader used a faulty hyperdrive in the future as well, to limit people's range of travel. Steering someone to a desert for repairs is easy when it is the only planet that "happens to be in range" when the hyperdrive goes out.
With only ONE PERSON (Watto) having parts for their ship, Common on Naboo but not many other places, it was easy to see where they would go.
I'm sure convincing Gardulla the Hutt who to sell the two slaves to was easy as well. I do find it strange though that Toydarians and Hutts BOTH being IMMUNE to force persuasion, they were chosen to watch over the two slaves. Sidious Could however have use money or power to influence the Hutts.
Sidious, being strong enough to keep the ENTIRE Jedi Council from knowing he was force-sensitive, could have easily influences people close to the Hutts to indirectly influence them as well.
Immediately making friends with Anikin was NOT just grasping at an opportunity, it was pre-planned! Yoda was aware of some forms of dishonesty in close proximity (watch his facial expressions when Sidious is talking!) but was still clouded from knowing exact intent. Anikin was "groomed" well away from watchful eyes and ears. And was made to APPEAR to be the chosen one. Sidious influenced Kenobi enough to make him want to help Anikin. Sidious probably used SOME influence on members of the council to make them doubt Anikin as well, JUST TO MAKE Kenobi more determined to train him.