time to transplant

i have 1.5 litre containers that i'm transplanting my 2 week old plants to. should i place the plants a couple inches lower so that i can cover up the stems as they get bigger or right at the top so they have plenty of room to root? also, for watering - do i saturate the plant and then let it dry out before watering again. most people seem to water every 48 hours. but how much are you watering them each time?

If i have extra stem i usually bury it...but, i move from 16oz cup to 1 gallon pot to 3gallon... as for watering, yes u saturate it and once its all dry repeat...

My mom told me not to bury the stem, or the roots will grow up- which, I am left to assume, is bad.

no they will not grow up. why are u transplanting into a small pot. u might as well go to at least a gallon better 2 or 3. that will save u from doing it again in a couple of weeks. and yes let it dry out u will be surprised how little water they need. rule of thumb when u think its dry wait at least another day.,