The SQO/SQI is better suited for machines with lots of discrete I/O that tend to step through the same large number of steps in about the same order over and over. Using the SQI/SQO pair can make troubleshooting much easier if done correctly, however, I prefer not to use those instructions due to some limitations in their behavior. Instead, when called for, I use MEQ/MVM or MEQ/MOV with indirect addressing, and have separate logic to control the sequencer step value.
With that said, and looking at your description of the problem, personally speaking, I would not use the SQO/SQI instruction for this type of application.
Using an individual bit for each silo is simple enough when each silo must be configured to accept material A or material B, but what happens when along comes material C?
What if there are other reasons to skip over a silo?
Those can be combined in ladder logic, pretty easily, but once you get to 4 or more different material types, then you will want to look into using an integer to store the material type for each silo.
To better help you construct the code for the application, it would be useful to know more about the filling operation, how many carts there are, how do you know where they are, etc (a picture added to the thread is always a great way to kick start the idea train, even if it's a crude sketch).
For examples of SQI/SQO pairs:
http://forums.mrplc.com/index.php?app=downloads&showfile=854
For state machine logic (might be useful to you):
http://www.plctalk.net/qanda/showthread.php?t=52654&highlight=state+engine
Welcome to the forum!
Paul