Hello Pal,
You are right ... If the same frequency band is reproduced by the main speakers & the subwoofer, it will impact the sound quality to some extent. To avoid this, I suggest you to go for a bookshelf/subwoofer combo instead of floorstander/subwoofer combo.
Generally (Not in all the case), when compared to a floorstander the mids & highs are a little more detailed & sweeter in a bookshelf.
Assuming that you have a bookshelf pair and a subwoofer, the subwoofer's frequency limit should be set properly i.e. for e.g. if your bookshelf's midwoofer can go maximum upto 40 htz low, then the subwoofer's frequency level should be set in such a way that it will only reproduce frequencies from 40htz and below. By this proper setting, you will get a complete bandwidth and the overall sound will be just great. (A pair of Wharfedale's Diamond 9.1 bookshelves and Wharfedale's SW150 subwoofer (Approx. 30K for the combo) would be an excellent choice and this combo can simply outperform almost many floorstanders in this price category)
Connecting the subwoofer to a Stereo (two-channel) amplifer .....
Connection Method 1
1. The subwoofer's "High Level/Speakers In" terminals have to connected to "Speaker A" in the amplifier.
2. THe bookshelves have to be connected to the subwoofer's "High-Level/Speakers Out" terminals.
Connection Method 2
1. The bookshelves have to connected to "Speaker A" in the amplifier.
2. The subwoofer's "High Level/Speakers In" terminals have to connected to "Speaker B" in the amplifier.
Connection Method 3
1. The bookshelves have to connected to "Speaker A" in the amplifier.
2. Using a 2RCA cable, the pre-outs (left+right) of the amplfier have to be connected to the "Low level (line-in) terminals" in the subwoofer. The length of the 2RCA cable will depend on how close the subwoofer is placed from the amplifier.
For PASSIVE subwoofer - connection method 1
For ACTIVE subwoofer ...
a. Integrated amplifier with only "Speaker A" and without additional "pre-out" - connection method 1
b. Integrated amplifier with only "Speaker A" and with additional "pre-out" - connection method 3
c. Integrated amplifier with "Speakers A+B" and without additional "pre-out" - connection method 2
d. Integrated amplifier with "Speakers A+B" and with additional "pre-out" - connection method 1 or 3
e. Pre/Power amplfier - Preamp with additional pre-out - connection method 3
f. Pre/Power amplfier - Preamp with additional pre-out & Poweramp with "Speakers A+B" - connection method 1 or 3
g. Pre/Power amplfier - Preamp without additional pre-out & Poweramp with only "Speaker A" - connection method 1
h. Pre/Power amplfier - Preamp without additional pre-out & Poweramp with "Speakers A+B" - connection method 2
Setting the VOLUME level of the subwoofer (Applicable only for ACTIVE subwoofers) ...
Step 1: Set the correct frequency level in the subwoofer.
Step 2: Keep the subwoofer volume level to minimum (0).
Step 3: Play a track and increase the volume (just 1 or 2 notch and not more than that) in the amplifier.
Step 4: Now, slowly increase the subwoofer volume level to match the output level of the bookshelves. When you feel that the overall sound is balanced between the bookshelves and the subwoofer, just leave the volume level of the subwoofer at that point.
Step 5: Now you have to use only the master (amplifier's) volume control to increase and decrease the hearing level.
Cheers

Ramesh