Firstly I am not hijacking anything and secondly I had not mentioned sound cards other than the DSP made by others as an alternative, given you merely stated that the minidsp was best, with nothing to back that up.
I was trying originally to answer
Polish023 question, by stating use your ears to start with, given that your ears are what you will be listening to the media with.
Having your bass/subs under your speakers is fine, but it all depends on if you have them on the floor or not and what that floor is made from. Don't forget bass is not directional as such so where you have them is not that important in a house.
What type of sub is it ?
Is it a downward facing reflex speaker or is it a forward facing reflex ?
Is it carpeted or hard floor ?
All these things will create a different sound and it would be best to ask others what experience they have had with the different materials used. I have seen many different systems used by different people, who in the end, tweak the system to how they like the sound. This even goes to raising a sub further away from the floor to alter the tone.