I'm glad you have asked this question, as I was checking some of my milk jugs and some of them that haven't germinated are beginning to look on the dry side, so I was going to bring them inside for a while and sit them into a container that has a few inches of water..and stick them back out again. Bottom water only is what I have been reading on the forums.

What about when it rains and goes in through the tops of the milk jugs, will that harm the seeds?

I haven't had to water my containers until recently when I've needed to open them up more as the weather warms. But the couple of times I've watered, I poured an inch of water into the tray my containers are in and they soak it up from the bottom.

Yes, rain and snow will enter through the top but the amount isn't that much and the extra will drain out from the bottom (and sides if you also put holes there as I did). But if your containers are waterlogged, then you will need to move them to another location to dry out.

Rain and snow getting into your containers is good as the mix will stay moist. That moisture helps with stratification as well as germination. I have not had any problem with too much rain or snow getting into containers. Perhaps in areas where it rains more that could be a problem. Most springs I have needed to water my containers.

I tried using a wand to water inside through the jug opening which didn't work too well. Either it pushed seeds to the sides or created holes in the mix or didn't get enough in to moisten completely. I also used a spray tank so I could put the wand into the container opening but that took too long as I had hundreds of containers. Bottom watering works the best for me. I use a container that holds many jugs at the same time. I put enough water in the container to just below the level of the mix in the jug. Put in the jugs and go do something else. Return and repeat until all are watered.

Once the tops are off and the seedlings are growing well I water with a wand set on light shower.

This year I am bottom watering my milk jugs in a kiddie pool. I can do about twenty at a time this way. I left them in there for half a day or an entire day and then swapped in the next batch. I tried top watering last year and it was aweful. Bottom watering this way is much easier for me and more effective.

how can you tell if water is being soaked all the way upto the top or upto the root when watering from the bottom. Does the soil color chages as if you were to spray water from the top?

put your finger in the soil

I have sown in milk jugs in the past and pop bottles - I cut them in half and duct tape one side down, or sort of cut slits so the tops will slide right on top of the bottom of the container, cut drainage holes and take the lid off. To date I haven't had rain or melting snow harm the seeds that I can tell, but it does help allow moisture in so that I water less. The only thing I've had to watch is if we have a particularly wet spring I'll move them somewhere under an overhang or something around the house so they don't get TOO wet. When I water I just open the jugs and use the shower setting on my hose. Usually if I see condensation during the day on the lids I know it's moist in there and warm too.

Right now my favorite containers are clear plastic cups tucked into zip lock baggies with air and drainage holes. In that case I just open up the zip locks and go outside with a jug of water and water each cup a little.

You can tell because the top of the soil will be dark and the jugs are very heavy.

I have milk jugs with a flap cut out of one side, so they are one piece. I can water them through the flap, but I find that with a nozzle set on 'Cone' I can use the hose, very effectively to water through the hole at the top and it is very fast that way. I just came in from doing it today. It doesn't seem to disturb the surface of the soil, because the cone setting on the nozzle sprays the water out in a circle, so it hits the sides of the milk jug and fills with water. I find that the easiest way yet.

I tried cutting the jugs and using the duct tape one year and I found it to be a LOT of trouble and this way is much easier to me. I can open the flap to sow or water and when it gets warm. It's easier to move them by the handle when you want to and I don't find any critters getting into them. And NO tape. :-)