You will fly between camps on light air transfer planes. Very easy and lots of fun.
Definitely NOT a mistake to book Singita Boulders instead of Ebony. I much prefer the atmosphere in Boulders. IMO, if you want to combine lodges I'd add a stay at Royal Malewane in Thornybush and/or Lion Sands Ivory Lodge (only the Ivory lodge, not the River Lodge.) These would give you the best Kruger has to offer.