On the TD-50 and TD-50X, the front panel MIX IN jack is for consumer audio playback devices, such as a smartphone or music player. The rear panel MIX IN (STEREO) jack is for electronic instruments, such as sampling pads.
Both jacks can be used at the same time. The [MIX IN] knob on the front panel, and the MIX IN Gain setting in [SETUP] > [OPTION] > [MIX IN], control the input level for both jacks together.