The interplay between Cooper pairs and Bogoliubov-de Gennes (BdG) quasiparticles is a topic of considerable interest in the quantum properties of solids, but its important ingredient, the sufficient amount of low-energy quasiparticles to interact with Cooper pairs remains elusive in conventional superconductors. Here a gapless superconductor with coupled paramagnetic atomic layers is used to generate a significant amount of zero-energy quasiparticles that Anderson-localize and bifurcate into regions of high and low zero-energy quasiparticle density of states. The enriched zero-energy quasiparticles induce puddled superconductivity and Josephson vortices. This discovery not only advances the understanding of the mutual interaction of Cooper pairs and BdG quasiparticles but also opens a new avenue for exploring and controlling exotic quantum phenomena where superconductivity, disorder, and spin degrees of freedom are entangled.