amd - I used to water the same way you're watering now. Try not to water until you see excess leaking out of the bottom. If you soak the entire potted soil in water, you're not only going to choke off the roots of much needed oxygen, but you'll also rase the TDS at the bottom of the pot (or, total dissolved solids making the PH at the bottom of the pot more unstable than the PH towards the top).

I don't know how big your pots are and that's also a factor, but I've learned pretty recently that you want to water when you can pick the pot up by just a few fingers. You also want to wait until the top most portion is dry and the bottom is just a little damp.

Your goal is to have a constant flow of water flowing from the top to the bottom over a period of time but very consistantly. Also, try not to let the water run over the sides of the soil into the very bottom of the pot, this can also knock the ph balance off.

Interestingly enough, I had a few roots on top of the soil the last time I transplanted which made me research the situation.

I found out that some plants grow "air roots" when the bottom roots don't get enough oxygen. sometimes this can also be caused by transplanting a stretching seedling up to it's neck in soil, because new roots start devloping where the covered stem now is but they aren't as developed as the lower roots.

How often are you watering? Do you have large enough drainage holes on your pots?

To get oxygen to the bottom of my root system after I overwatered my babies, I used a few chopsticks and very slowly stuck them through my drainage holes (I had just transplanted so I didn't have to worry about penetrating any roots and snapping them) and made a cross shape so the tunnels I made meet eachother.

Just a suggestion.

I haven't ran into a pot that I haven't had to enlarge the drainage holes for oxygen.