Predictive maintenance of rotating machinery increasingly relies on vibration signals, yet most learning-based approaches either discard phase during spectral feature extraction or use raw time-waveforms without explicitly leveraging phase information. This paper introduces two phase-aware preprocessing strategies to address random phase variations in multi-axis vibration data: (1) three-axis independent phase adjustment that aligns each axis individually to zero phase (2) single-axis reference phase adjustment that preserves inter-axis relationships by applying uniform time shifts. Using a newly constructed rotor dataset acquired with a synchronized three-axis sensor, we evaluate six deep learning architectures under a two-stage learning framework. Results demonstrate architecture-independent improvements: the three-axis independent method achieves consistent gains (+2.7\% for Transformer), while the single-axis reference approach delivers superior performance with up to 96.2\% accuracy (+5.4\%) by preserving spatial phase relationships. These findings establish both phase alignment strategies as practical and scalable enhancements for predictive maintenance systems.