For germination, all I did was wrap my seeds in a moist paper towel. By moist I mean the paper towel is wet to the touch but not soaked. Put the paper towel in a baggy or something and put that under your sink (or any other dark place for that matter).
after about 24-48 hours you should see a white root popping out. When you plant it in the soil, put the root DOWNWARD into the soil.
I immediately put my newly planted seeds under light, and I never had problems with the plants being in completely different cycles. They were all within the same place as far as growth goes throughout the entire beginning process.
I'm not sure of the advantages/disadvantages of just putting your seeds in water - but I know that if you have really hard seeds, it's harder for them to break open with less moisture.