Using this method to germinate very small seeds is a little chancy. The radical or root which grows first attaches to the wet paper and will break if pulled loose. In this case cut the paper towel with the seed attached and plant it with the seed into a good seed starting mix. The general directions for germinating in wet paper are simple. Wet the towel or paper coffee filter and squeeze out excess water. Spread seed on wet paper and fold paper up with seeds. Place paper in a ziplock plastic bag and place in a warm place about 70 degrees for most seeds. After three days check for seed germination. Reseal and check every day after that until germination is apparent. Al

I defintely prefer coffee filters to paper towels. Additionally, I fill a spray bottle with water and hydrogen peroxide diluted 10-1 for misting every 3 days or so.

While there are drawbacks to this method with teasing the young, fragile root hairs apart and transplanting, I find that it is the best method for tough to germinate seeds like certain lupines and CA sages and heat lovers like peppers and melons. It also allows you to avoid damping off and other moisture-related problems with both soilless and potting mix germination in flats or other containers.

So after the seeds have germinated and I put them on the potting soil, should I top them with more soil, or should I leave them on the top of the soil?

Depends on the seed. If in doubt sprinkle a little vermiculite to cover. Al

I double the vote on the coffee filters, they are cheaper then PTs, and they hold up much better then PTs.
Covering the seed does depend on the seed, also how you handle the seedling depends on the size of the seed.
I had some teeny-tiny seeds this year, when the long root got fairly long (which didn't take long) I put my soil in the planter I was using and made holes with a pencil and rounded out the hole to make it large enoungh to not hurt the root. Then I held the leaf part and aimed the root for the middle of the hole, I gently pushed dirt in around the root and watered gently so the water finished filling the hole and made sure there were no air pockets. BUT I caution, you have to be VERY VERY gentle in doing this so you do not disturb the root. Also, some seedlings may not live longer then a day or two if you don't get them planted soon enough. This method takes practice, and what works for someone else may not work for you, so you have to experiment with your own seeds and work out your own techinque. I like starting larger seeds this way, for me it is just easier to handle them and I can plant them where I want them once they have germinated.
It might work better for you starting out to use vermiculite to cover most if not all of your germinated seedlings, or a soilless mix until you get used to handling the young babies, you won't need all of your plants usually so you can experiment with a few after you have treated the ones with care you plan on keeping.
Experimenting is the key to this method if you haven't started many seeds. Take notes on what works and what doesn't and before you know it you will be able to start many seeds this way, with success in growing them to maturity.
Good luck, Fran

What I'm using is a thin large plastic pill bottle. I cut the top off, put grooves on the neck, inverted and put inside. I have about .5in of water on the bottle. Filled the neck with potting mix, moistened and added more potting mix, put the seeds and then more mix. I'm using a straw to put more water in as needed. If I wanted to be really gentle when its taken out I could just cut away the bottle.

Dicot, have you tried chipping the seed coat on lupines? After I learned how to do that, every type of lupine I've tried germinates in 2-3 days (shrubby types, perennials, annuals, etc.). I take a very sharp knife, and knick the edge on the opposite side of the seed from where the root sprouts (there's usually a white dot on the side of the seed where the root comes out). Often you'll see green just peeking through from where the seed coat has been chipped. I'm sorta crazy for lupines, so learning that from a friend was one of the most useful things I ever learned on starting seeds!

--Ron

Most of you know this, but it's worth stating: when you plant it the radical or root which grows first should be planted DOWN. It is a root, after all, and not a stem.

I plant seeds with my third graders every year and you would not believe how many of them want to plant it root side up.

Lemecdutex, I've never had much luck with scarification of any seed coat. The baggie method is so easy for germination that I seldom try anything else these days. Soaking the lupines for 4 hours in warm water helps too.

Some seed is completely impervious to imbibing water until the seed coat is mechanically damaged or scarified. With small seed I roll them between two sheets of course,36 or 40 grit sandpaper until a wearing through is noticed. Al

Sandpaper is a neat trick! I had not thought of that. I think I will try it. I had wondered how you deal with small seeds.

I have always kept some rough 'wet/dry' emery paper from the auto refinishing section of the parts store for scratching seed.