The Borg are powerful but are lacking in tactics, though they should have the collective tactics of thousands of species. The Borg were having trouble fighting Species 8472 because their primary tactic of assimilation did not work. We see Species 8472 destroying Borg worlds but what kind of damage was the Borg really capable of doing to Species 8472's universe. The Borg wanted to use nanoprobes reprogrammed by the doctor to end the war, but in my personal opinion they really did not need them. They needed them to be able to assimilate species 8472 but not really to win the war. The reason I say this is the Borg have WMD's. They wanted to use a multikinetic neutronic mine with a 5 million isoton yield capable of destroying an entire solar system with shockwaves that would scatter the nanoprobes over a 5 light year radius (Voyager episode Scorpion).
Species 8472 most powerful attack was destroying Borg planets. There were several other technologies in the Star Trek Universe that the Borg had come into contact and should have assimilated. Some WMD's that the Borg should have are trilithium warheads that cause suns to go Nova (assimilated federation ships), genesis device which mass terraforms planets incredibly fast (again assimilated ships that would have info on this), large quantities of antimatter (have a lot and it would be capable of destroying most things), and time travel (assimilated Federation ships, used time travel in movie, and assimilated Kremlin -people who in year of hell episode were wiping species out of existence one of personalities 7 of 9 had in another episode was one of them). Considering the massive amount of WMD's the Borg have if they were also attacking Species 8472 in fluidic space Species 8472 would be in a worse position than the Borg were. Destroying a billion Borg or hundreds of Borg worlds should not matter since they can always get more and the individual doesn't matter. Though a question does come about can species 8472 destroy the Borg faster than the Borg can assimilate other species (particularly if they begin assimilating species considered inferior and not worthy of assimilating) while the Borg also attack their dimension?
Considering the resources and abilities that the Borg have Species 8472 should not be able to destroy them. The Borg operate in multiple dimensions. They invaded species 8472's universe (Fluidic Space) and have been in other universes as well. Supposedly the Borg acquired autonomous regeneration sequences from species 259 which we are told come from Galactic Cluster III which is said to be a transmaterial energy plane. They likely would be sending Borg ships to other galaxies and through time itself. By evidence of the Borg technology they should be spreading through out dimensions, time, and ever outward. Though they would also be ignoring species that they do not see as having anything to offer the Borg on it's quest for perfection. Also if just a few ships manages to get away be it through time, space, or into another dimension the ship should be able to recreate the collective.