Unfortunately, no update to AN3330 is currently available but the following may help:
The SSD module on the MPC5606S is actually an enhancement of the module on the S12(X) with the difference that the previously software-controlled process of blanking-then-integration is now automated with counters that control the length of blanking and integration inside the SSD module itself. In general the CPU will simply configure the SSD then start the step and leave it to complete automatically.
This being the case you should be able to reuse your previous configuration settings by adjusting them for the BIS to use.
To get a feel for what the BIS does compare flow chart Figure 16 in AN3330 with Figure 36-12 in the MPC5606S RM Rev 5. There's also a description at 36.4.2.2 that describes the BIS operation. The RM has a note on using the SSD in "legacy mode" which is the S12 mode of operation.
The registers to set will be:
CONTROL = configure the module
BLNCNTLD = blanking count (how long does this phase last)
ITGCNTLD = integration count (how long does this phase last)
PRESCALE (for the counters)
IRQ for interrupt enables
CONTROL.B.TRIG to kick off the step
The status bits in IRQ will tell you when each phase in the step is complete and if an accumulator overflow occurred
For the SMC there is a dedicated app note AN4037
