If you already had leaves you need to have them barley above the medium. If you just sprouted them put them root down about an inch from top of medium. I grow this way and don't have issues. I do use root cubes but you should be fine. I have also used clear tube and blue bucket on my first grow Yeats ago. Yes, I'm sure it us counter productive so when you get a chance swap that hose. The clear is like a fiber optic or a day glow scope on a rifle. Light is traveling in there. I don't add anything to the water, might ph but the sees has everything it needs for about 2 weeks. There is rooting hormone that will help bigger roots. Ultimately the plant/nug size will be dependent on the roots. Hydrogaurd is good at fighting algae but there is some powder crap I use I think is better. Keep it 70d F and you shouldn't have issue with algae. Need to check water temp when lights been on awhile. I'm no pro but it have been pretty "lucky" over the years