You have been misinformed. The commnd rate (1T or 2T) has nothing to do with how many DIMM modules you use. S939 requires 2 modules to run in dual channel mode which is the only reason to buy S939. Anybody running a S939 with a single module is wasting his money big time.
Most S754 boards have 3 sockets for memory. Yours has only two because it is a microATX board so they are cutting costs. If you have a good chip you can run all 3 populated, but may have to run 2T in order to run at DDR400 (PC3200) speeds.
Two modules will run at full speed with no problem! I don't recommend 1GB DIMMs though. Stick to a pair of 512MB, or even 256MB (1GB or 512MB total) if you want the best performance. Only go 1GB if you are a hardcore gamer or work with very large images or other extremely large files. For most others 1GB is overkill.