You want the chemical-laden water to reach every single nook and cranny. Nevertheless, as the service professional, the problem is yours. You can make up for hydraulic deficiencies by more brushing, more vacuuming and possibly making hydraulic improvements, such as directional return fittings or diverter valves that can properly balance the suction between the skimmer and main drain and the return lines. You can also treat the problem by applying chlorine granules directly to the algae areas or rubbing the area with a trichlor tab. There are tools designed specifically for this purpose.
Chlorine is a highly effective spot algicide.
You might also try placing a chlorine tab in a plastic bag, cutting a few holes in the bag and hanging it in the water near the algae-affected area. Don't do this in a vinyl pool or near any surface that can be bleached by the chlorine. Finally, purchase an algicide that is especially designed to fight black algae. You may have to do some testing until you find the one that meets your specific needs, but as far as we know, there is no strain of algae that is totally immune to chlorine and all commercial algicides. Make note of the type of algicide you are using until you find one that works for you.