I always counted on HT in a box systems for my DVD viewing until a friend of mine started working in an electronic store lately, he gave me an employee discount on one of the offers they have in the store, so i bought the set and took everything back home, read some manuals, searched through this forum and started the installation process;
Onkyo TX-SR605 AV Receiver
2 pcs. Wharfedale Diamond 9.5 speakers for Front Left & Right, 1 pc. 9CS for center, 2pcs 9.1 for surround and SW 150 for sub.

I used the Audyssey Automatic speaker setup and I end up having the following speaker configuration: Front , Center & surrounds are in Full Bandwith, LPF of LFE 80Hz, Double bass On. Having this configuration, I feel that the bass was unatural and a bit much boomy. Some advice to put all speaker to small and LFE to 80Hz as per THX reccomendation however I dont have large and small option on my Onkyo TX-SR605, I have to choose from Full Bandwith, 40Hz, 50Hz ... to 200Hz. Which frequency should I choose if I want to set it to small. Another thing that is confusing me is that there is another crossover frequency control on my subwoofer (it ranges from 35-85), which frequency should I use? can somebody help me please!

Onkyo TX-SR605 AV Receiver
2 pcs. Wharfedale Diamond 9.5 speakers for Front Left & Right, 1 pc. 9CS for center, 2pcs 9.1 for surround and SW 150 for sub.

I used the Audyssey Automatic speaker setup and I end up having the following speaker configuration: Front , Center & surrounds are in Full Bandwith, LPF of LFE 80Hz, Double bass On. Having this configuration, I feel that the bass was unatural and a bit much boomy. Some advice to put all speaker to small and LFE to 80Hz as per THX reccomendation however I dont have large and small option on my Onkyo TX-SR605, I have to choose from Full Bandwith, 40Hz, 50Hz ... to 200Hz. Which frequency should I choose if I want to set it to small. Another thing that is confusing me is that there is another crossover frequency control on my subwoofer (it ranges from 35-85), which frequency should I use? can somebody help me please!
I will try to help conceptually here, although I must admit that I am not familiar with the specifics of setting up Onkyo receivers or Wharfedale speakers.

"Large" and "small" are all about re-directing bass to a subwoofer from speakers that can't handle it properly. I can see your 9.5s being set to full bandwidth. But, I suspect you will be better off sending some of the bass from the center and surrounds to your sub. As the Onkyo appears to lack a large/small speaker option, I believe full bandwidth would mean large. Assigning a crossover frequency would be the same as setting the speaker to small. The speaker manual may recommend a crossover frequency. If not, try 80 and adjust to your taste from there.

Since you are using your receiver for bass management, you want to disable that feature on the sub. Your SW should play whatever it gets from your AVR.

BIslander is correct on all points. Let me add that you might want to consider retrying Audyssey after reading the admittedly intimidating 'official' Audyssey thread here. There are hints and tips about doing it right and most user's manuals give the erroneous impression that it is impossible to get wrong.

How do i disable the bass management on the sub? on the back of the sub there's only a volume nob, crossover frequency nob "no way to turn it off" (min 35hz-85hz max) and phase switch (0° or 180°).
I read the official thread before running the Audyssey setup and did what it says, put the mic on a tripod, turned the A/C off and left the room completely.
One more thing, why do i get no subwoofer output in 2-channel mode? should i connect the front speaker to the speakers level input on the sub for that to work?