When Sherlock looks down before he jumps you can see a trailer or an open back of a truck full of bin bags. My guess is that he jumped into that. He made Watson stand on a specific spot, which I would guess obscured his view of the footpath. Watson is disorientated from being hit by the cyclist, which I would bet is one of Sherlock's irregulars (who had been mentioned for the first time this season earlier in the episode) and is kept away from Sherlock by the doctors/nurses.

I would also guess that what Sherlock asked of Molly is to help him fake his death by declaring him dead.

Other people have speculated that he tossed Moriarty off the roof in his (Sherlock's) coat and had Molly and Mycroft cover up and declare the remains were Sherlock's, But I don't see how Watson would have confused the falling body for Sherlock.

Also it could have something to do with the Dummy Sherlock had hanging around the flat at the start of the episode.

And it should be mentioned that there will be a third season. Both Moffat and Gatiss have confirmed that it was commissioned at the same time as the second.