Despite intense theoretical and experimental investigation, the physical mechanisms governing the suppression of bound quark-antiquark states in nuclear collisions are not yet fully understood. While color screening in a plasma phase is expected to play a role, there are numerous other possible suppression mechanisms that do not require deconfinement, as well as effects on the heavy quark initial state in the nucleus which can also play a role. To study these effects, the PHENIX collaboration has used the flexibility of the RHIC accelerator complex to observe the evolution of open heavy flavor and quarkonia dynamics as both the projectile and target nuclei size are varied. Open heavy flavor in small collision systems can serve as the baseline for interpreting quarkonia production in the nuclear environment, and comparisons of the ψ(2S) with the ψ(1S) show that in rapidity regions with relatively high hadron density, the larger 2S state is preferentially more suppressed than the more tightly bound ψ(1S). This suggests that late-stage mechanisms may be at least partially responsible for quarkonia suppression in nuclear collisions. In this talk, we will present results on excited-state quarkonia in p+p, p+Al, and p/d/3He+Au collisions and open heavy flavor in small systems, and discuss how these measurements impact our understanding of heavy quark behavior in the quark-gluon plasma.