Bek,
The only good algea you really want to worry about encouraging is coralline algea - the purple/reddish crusty stuff that covers the back of your tank.
If the algea is buried and not on the sand bed itself then I'd not worry about it. I had someone pretty knowledgeable tell me that if it is buried down there then it is contained and it is sucking up the bad nutrients out of the sand bed.
What I've expereinced is that if the water flow changes then I get a bit of cyano popping up and I have to change the water flow to make it disappear.
If it is buried and not on your sand bed I would leave it and just keep an eye on your tank.
I would not worry about the growth of your macro's in your refugium - they will grow regardless of the changes you make based upon cliffrouse's suggestions. The growth will just slow down.
If you have Macro's in your main tank then I'd make sure you trim them back and keep them away from corals. I'd be very worried about them growing @ a high rate then deciding it was time to reproduce because it is such a great environment.
Lastly - how deep is your sand bed?