Personally, I would leave your skimmer on. Most hobbyists do and it does not seem to reduce the effectiveness of AF.
From the manufacturers site regarding the fresh water version of AF, and we have been told it is the same:
"Pond Care AlgaeFix controls algae in two ways. Many algae, like Chlorella, consist of a single cell. Pond Care AlgaeFix causes the algae cell wall to leak. The algae respond much like a deflating balloon. Other algae, such as Oedogonium, form filaments made up of many cells. Pond Care AlgaeFix binds to protein in the cell membrane, disrupting the flow of nutrients and ions across the cell membrane. Filamentous algae respond to Pond Care AlgaeFix by gradually disintegrating over time. AlgaeFix can be used with aquatic plants."
Since the siphoning algae can repair their cell membrane so easily compared to many algae, I assume that this may be the reaon that AF does not work well on many algae.