is if the algae is in you trough can't it seed and spread into your tank.
No it can't, the algae is already all over your tank.
If you see it anywhere, there are spores everyplace.
The idea of an algae trough or lighted refugia is to give the algae a better place to grow than on your corals. In my trough the water is only a half inch deep, it if flowing fast and it is right under the main tank lights.
It sits to the rear of the tank above the water so some of the spill light goes into the trough. The thing is made out od a Home Depot 4"X4" PVC fence post sliced in half. It is also on a slight angle so the water flows from the input to the tank. There is a window screen in the trough which had some Sakrete Mortor mix smeared on (algae loves that stuff)
My trough is fed from my skimmer and uses no power. The lower end of the trough is just at the water surface so it does not splash.
Algae is self limiting and only so much can grow with the nutrients in your tank. If I get too much hair algae in the trough, I roll up the screen and scrape it off in a sink.
It is usually filled with hair algae but there is absolutely none in my tank