The problem I have is that the clogging is at the end of this tube which you also have above the water level.Nope it will work either way. I've done it both ways.
I have the tube off the bottom so it's closer to the water level, just so it isn't so loud when trickling into the sump.
Its like some kind of "clot" is being built there.
Thats why I thought it might be better to have no tube there.. but yeah.. when the ATO is still flushingit, there shoul be no problem I guess...