I use tweezers and gently transfer them to the growing medium.

Try not to touch the radicle. Pick them up by the seed. Or cut out a piece of the paper and handle that.

how long do you leave them in the paper towel. I can see a very tiny root. ?

I have had bad luck leaving them in too long. Root plants itself in towel. Should I be planting the towel and the seedling?

i use tweezers and gently put them in growing medium. there shouldn't be a problem with planting them along with the toweling if you need to. I sprout tomatoes and peppers this way. Bill