What is an EBA? For the flying foxes I have an acara in the tank as well will they bother each other? How many do you have in your tank? Do you feed them anything else? What do you mean by they are a tad bit messy? Will they eat the plants?
EBA = Electric Blue Acara (the common abbreviation here for this fish
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). Flying foxes will completely mind their own business. They will most likely ignore other fish completely. I used to have two (I don't anymore), but they can school as juveniles (old fish tend to be loners). Mine didn't squabble much, though (occasionally, there was a scuffle, but it was minor and usually nitpicky, lol). If you get young busy bees, they may be a nuisance to your much slower and sedentary bichirs, kind of like Pictus catfish with Discus. However, older flying foxes shouldn't be a problem.
If the algae was low, I fed them Algae wafers. Sometimes, they would eat the flakes, among other food I dropped in the tank for the other fish. They are a bit messy, meaning they eat a lot of green stuff, and you know it through their stools. Their stools are quite obvious in color, sand or gravel. But it may not be as much of a problem on dark-colored sand or gravel.
They won't eat your plants. Also, Siamese Algae Eaters and Siamese Flying Foxes are two different species of fish. They are nearly indistinguishable, but they are different. If I remember correctly, SAEs are larger, while flying foxes are smaller, and their band/bands are in slightly different places.