Trump took on Manafort because Manafort was the go to guy to counter the delegate stealing that Cruz was pursuing at that time in the campaign.
If you look at it one way, with the idea that the Clinton campaign wanted Trump to win the nomination, the plant hypothesis would make sense.
Manafort resigned as soon as Russia/Ukraine allegations started flying around.
It could be that Trump used Manafort, even if Manafort was a plant, because it actually helped the Trump campaign and backfired on the Clinton campaign.