The emission of conjugated polymer nanoparticles (CPNs or Pdots) is often tailored for specific uses by functionalizing CPNs with dyes that act as fluorescence resonance energy transfer (FRET) acceptors. A number of dye functionalization methods for CPNs have been developed, ranging from simple noncovalent doping to covalent attachment. We seek to develop guidelines for when noncovalent doping is acceptable and when covalent attachment is necessary to achieve the desired result. We present results of CPNs functionalized with photochromic spirooxazines by four different methods: simple doping, doping with an amphiphilic coating polymer, covalent functionalization prior to CPN formation, and covalent functionalization after CPN formation. The different CPNs are evaluated in terms of their fluorescence photomodulation properties to determine how the preparation method affects the CPN-dye photophysical interactions. Doping preparations yield the most efficient quenching of CPN emission due to shorter donor-acceptor distances in these CPNs compared to those with covalently tethered dyes. Aging studies reveal that the photochromic dyes in doped samples degrade over time to a far greater extent than those in covalently functionalized samples. These results suggest that dye-doped CPNs are appropriate for short-term experiments where highly efficient FRET is desired while covalent dye functionalization is a better choice for experiments executed over an extended time frame.