Line Out vs Parallel

[Sotm31]

I have a Polk PSW404 with a Polk Sound Bar. I am inquiring on whether to hook up to my Subwoofer out on my Yamaha receiver, and if I do what frequency to set it to, or should i just run the subwoofer parallel with the fronts? I know in the manual the first option is parallel, but there is an alternative set up using line out. Also, If I am setting all of this up manually, what levels should I use for the surround sound. I have a Yamaha receiver with a GUI interface that will set it up automatically, but I am reading not to do that, but I am getting no specific settings. Let me know what anyone thinks....... Thanks.
Proud Owner of Polk Sound Bar!