I too have been having a battle with algae of a different kind and the only thing not mentioned in the previous advice is the phosphate.
If you don't have a test kit for that, take a test tube of water down to the pet shop and get it tested, you might find part of the puzzle.
Best idea is to take a tube of plain tap water and a tube of tank water and compare the 2. I figure my feeding is to blame for excess phosphate in my water as it's clear when it comes out of the tap :oops:
My algae is making inroads to come back and the daily dose of flourish comprehensive seems to keep some of it at bay but I haven't managed to eradicate the main culprit staghorn algae yet - phosphate in the water is the last thing I am yet to conquer.
disclaimer: if your kind of algae is not affected by phosphate I'm sure the gurus will put me straight :lol:
-----
further, what is the benefit of starting the plants off in a small layer of water over starting them off in a full tank but without the fish?