A total of 25,600 3-inch PMTs will be installed in Jiangmen Underground Neutrino Observatory (JUNO) to achieve more precise energy calibration and to extend the physics detection potential. Performances of all bare PMTs have been characterized and these PMTs are being instrumented with the high voltage divider, underwater front-end cable, and connector. In this paper, we present a dedicated study on signal quality at different stages of the instrumentation. An optimized high voltage ratio was confirmed and finalized which improved the PMT transit time spread by 25%. The signal charge was attenuated by 22.5% (13.0%) in the 10 m (5 m) cable and it required the addition of 45 V (23 V) to compensate for the loss of PMT gain. There was a 1% overshoot following the PMT signal and no sign of reflection in the connector. A group of 16 3-inch PMTs with the full instrumentation was installed in the JUNO prototype detector together with a few 8-inch and 20-inch PMTs, which showed good stability and demonstrated a photon detection system with multiple types of PMTs.