How big are your seedlings??

The top watering kinda bites when the seedlings are still at the cotyledon stage. If your transplanting I am guessing that you have at least 2 to 3 sets of true leaves, if so I would say water from the top.

This is another reason why I do not bump up my pots!!

I haven't repotted many yet. The first I repotted were Nasturiums that were started in Jiffy peat pots. They are big enough to top water without any problems. But, it was with those that I first noticed that bottom watering wasn't as effective now that they were in the cups. I also started some geraniums seeds in wet paper towels that needed to be potted once they germinated into individual pots. These are the real problematic ones: I soaked those cups throughly before I replanted the seeds, but now they need second watering, and are too small to top water without moving around a lot & I don't think the bottom watering is working well enough. Hence, my problem ....

Yeah I know that problem all to well. A trick I do is I actually pour the water in my hand then trickle it on the seedlings, you may still have to adjust the seedlings but this method for me sure works better than dumping water on them.

After you get that first initial watering then you should be able to bottom water successfully. Another trick since you haven't replanted all of your seedlings try to water the soil you are going to transfer them to first. Then add your seedlings. Taking a wild guess here the reason the bottom watering isn't working is because mix straight out of the package contains air. That first watering elements the air, therefore allowing bottom watering to work.

Make sense??

I've also used a mister on my smallest seedlings with good results. The type that's worked best for me are $1 travel variety from Target or Walmart. Plenty of water per spritz but gentle enough to not blast a tiny seedling.