In general my recommendation when not using an auto calibration room correction is to go a low as you can, to where they sound correct to you, I personally prefer a more full sounding speaker, but this is my personal choice, your settings will have to reflect your individual taste and the way your room effects the sound of your speakers. This is how I do it by ear. And it will take some time and tweaking, but it will also help you in learning what the effects of these types of changes can have on your setup and give you a better overall understanding of these things.
First make sure your Sub setting (LPF for LFE) is at 120hz. (this should be the default)
Then make sure your distance measurements are as close as you can get them.
Your Surrounds and Rears will take less time so I'll start with those.
Surrounds and rears:
Those all have 3.5" drivers, and most likely the settings will be the same for both positions, I would suggest starting at 120hz, (because of the driver sizes) then as you listen to some content, try dropping to the next lower setting, re-listen, simply repeat this process until you think the speakers sound as if they are straining or reverberating too much (lower tones will get muddy or sound as if there is a flutter in the speaker) then simply set the crossover to the next higher setting from there.
Center:
Speaker Wire only, same listening rules apply, but in most cases with the CS-8040 HD you'll want to start with 80hz, and most likely you'll find that 80hz or 60 hz is best.
Fronts:
These will be a little different, with speaker wire only to the speakers (no RCA cable to the Low input) first set them to Large and listen to them like that for a day or so. (Unless of course you hear something obviously wrong) and adjust the dual in the back to get the bass output that you like.
Then after a this, go back in, set them to Small, with an 80hz crossover, again adjust the dial in the speaker to taste, and repeat the steps you took with the other speakers. Once you find the small setting that works best for you in your room, then after a day or so, change it back to Large and compare, just choose what ultimately sounds best to you.
With all these settings, since you set them by ear, there is the chance that all of a sudden something just sounds off with specific content, then just simply go in and tweak the settings a little, manual setups can take small changes over time, but your not going to hurt anything in the process, just don't get in a hurry and take small steps.
If you want any other setup help, placement, toe in, feel free to ask.
If you would like to experiment with other types of connections to your Fronts, also ask, but do yourself a favor and live with them connected with speaker wire only for a while, so you have a good feel for them when experimenting further.
Good Luck