According to the ATA Spec, they don't affect each other at all:
Advanced Power Management is independent of the Standby timer setting. If both Advanced Power Management and the Standby timer are set, the device will go to the Standby state when the timer times out or the device’s Advanced Power Management algorithm indicates that the Standby state should be entered.
So you can use -B 254 to not let the Advanced Power Management part of the drive spin it down, but still use -S 1 to have the Standby timer spin it down after 5 seconds.