According to a lot of seed companies, they prefer you to not use the paper towel or cup of water, although Ive been using paper towel method for a while.
They prefer you drop the seed directly into the substrate (soil, rockwool, plug, or whatever you are going to be growing in. The reason they give is that the taproot that sprouts is easily damaged on a microscopic level. The taproot will have tiny hairs that will stick to the paper towel and be damaged when you remove it, even though it looks fine.
I was skeptical of this so I did a little experiment recently and heres what my results were:
First its worth noting that germinating in temperatures ranging of 65 - 78 degrees, 50% success, ten days time......In temps 81 - 88 degrees 100% in two days!Most germination kits also have a heating pad so dont let your temps drop below about 78.
I planted six bagseeds each in the 81 - 88 degree temps, in to soil, paper towel, and an aerogarden peat plug. Not only did all of them sprout within 2 - 3 days, but the ones directly in the soil sprouted fastest (all within 40 hours) and are growing the fastest.
The biggest find in my experiment was the temperature. I did all this cause I was having trouble germing inside, then used the garage and its all good. Dark and warm, thats the most important factor.