Manafort came on because he was the best guy to stop the delegate stealing Cruz was involved in. Stone may have recommended him to Trump because he and Manafort go way back, so Trump would have trusted his judgment on the exact guy they needed at that moment.
That brings up the question if the delegate stealing was part of the plot to get Manafort on board and Lewandowski out. That would mean the plan to kneecap Trump was in progress even before he was nominated. It would mean that the dems wanted Trump as the candidate, as some people have theorized, seeing as Manafort did what he was brought on to do. It follows, as well, that the Ukrainian stuff that came out which led to Manafort leaving the campaign could have actually been a way to exfiltrate Manafort before he was sniffed out.
Trump went to Mercer after that and Kellyanne came on board as part of that package, IIRC. Trump must have figured it out at that point.