sean,
I don't always start plants from
seeds. In fact I'm quite impatient that way, so I often buy plants at the home improvement store (nursery), and just wash off the roots before transplanting them into the hydro system. But yes When transplanting that way I try to be careful with damaging the roots. I usually just submerge them into a bucket of water, and work the roots gently with my fingers to get as much of the soil off as I can. I also have the hose within reach, and with a shower head set at low pressure to further rinse the roots off with before transplanting. The roots can take damage, but the less the better. They call it "Love."
When I do start seeds, I just use a small plastic Tupperware container (with a lid to hold in moisture). and a wet paper towel at the bottom. I just set the seeds on the paper towel, place the lid on it and set in a warm place. Then check it daily. Once the seeds sprout, I place them in some type of
growing medium. If I don't the roots will attach themselves to the wet paper towel and be hard to separate without damage. The growing medium might be regular potting soil, or a growing medium like vermiculite. Potting soil wont require added
nutrients, but a regular hydroponic growing medium will. With seedlings (and/or sprouts), I start with about a 1/4 strength
nutrient. Either way, I will hand water them daily (as needed). I can easily build a setup that will do this automatically, but don't really start enough seeds this way to bother. I have some started now in fact, both in soil and straight vermiculite.