In order to see the spoolfiles generated by BPCS you need to have the proper rights to view the output, otherwise you are only able to see your own generated output.
So if you want to see the BPCS output generated on the iSeries through Navigator, either login with a user, who has the proper rights or get your UID upgraded to the proper rights.
I hope your question is answered.
Apart from authorisation issues you can modify the set of spoolfiles shown in Navigator. Under Basi Operations, Printer Output (Right click) and select Customize this view then select preferences.
There you can enter your preferences.
Remember that the authority of the user with which your Navigator session is connected to the i is determining what you can an cannot see.