The SeaFET and SeapHOx systems are designed to sample at a fixed depth. If you want to run discreet samples at depth intervals, you will need to find a way to move the system to a specific depth before each sample interval and stop the descent / ascent for the entire pumping and sampling cycle to get a valid CTD / pH / Oxygen sample.
If you are able to communicate with the system through the serial I/O during profiling, you can send a sampling command to the sensor at each depth point and allow it to complete its sample cycle. Consult the manual for each model for the length of time required to complete each sample. Once the sensor provides a sample, you can then move it to the next depth point and repeat.
If you aren't running real-time communications to the SeaFET/SeapHOx, you could also set it to autonomously sample at a time interval that gives you enough time to move the package to a new depth point between sample cycles. The challenges with this approach would be to know exactly when the sensor is sampling without any direct feedback from the instrument.