it really doesn't matter if the stems are in the water or not. they root either way in about the same time.

i use promix mixed with 1/3 perlite and 1 1/2 tbsp dolimitic lime per gallon of soilmix. the lime is absolutely necessary! promix is peat based so the ph is way to low for mj without the lime. that is the same soilmix i use all the way through flowering. make sure you get dolimitic(dolimite) lime, they also sell hydrated lime which is much stronger and easy to overdose!