The perlite would need to be mixed in, or at least underneath everything...to allow the water to drain out faster...it just adds air to soil, I always clone straight into my soil as well, albeit about 40% soil and 60% perlite and it works for me...but they always look like shit until the get their new leaves going...which takes awhile...the plant has to use a lot of energy to make new roots, so it saps everything it needs from the leaves and it tries to make roots...but overwatering will also look like this...so the question is does it have any roots yet or not..try to wait 3 days and then check...lol. I find that if I make myself wait 3 days from when I first want to check then I am less likely to hurt the poor thing...