My suggestion for using channels 3 and 9 was only if you had a piece of equipment that was specifically for WDS and supported transmitting/receiving on multiple channels and/or frequencies. If you're just using a standard wireless router (and from your comment I gather that you are) then you're right, you can only select one channel (although some routers/APs support a secondary standard channel in addition to the primary wide channel) and so you shouldn't have any issues with overlapping channels anyway, other than interference from other wireless devices in the area.
There normally isn't any reason to use a 20MHz channel unless you're using non-802.11n equipment or you have a lot of interference. If you are only using 802.11n devices, my recommendation would be to start with a 40MHz channel, especially if you need the additional bandwidth. (Which channel you start with doesn't really matter unless you get NetStumbler or something like it that can tell which frequency is the least congested.) If you're getting low throughput or problems connecting, try changing channels to see if it improves.