I bottom water mine.

I would get a fan on them if they are too wet and try to get them dried out.

I hope that helps.

Keriann~

I top water because I don't like holes in the container to make a mess on the window stool. I poke a hole in a bag with a safety pin to make a very fine spray and usually water along the edge of the container only, which makes most of the water flow down to the bottom and then spread from there, which has the same effect as bottom watering.

That seems like a lot of work. I have hundreds of seedlings and that would take me all day. : )

You are still missing the main advantage of bottom watering. The seedlings suck up the water they need, instead of us pouring water over them and seeing what pours through and what the soil soaks up.
I also believe watering from top encourages dampening off becuase the top is usually wetter than the bottom most of the time VS. bottom watering (top layer dries out faster and longer)
But hey, if it is working for you, thats great!

Keriann~