Here's how I do it.
First off I load the song up in Audacity and trim off the intro section that I don't want. Then I save the audio into a new song folder in StepMania. Next I open DDReam Studio and use it to approximate the BPM of the song. Then I open up StepMania and open up the song in edit mode, set the BPM I found in DS and put in some dummy arrows as quarter notes and adjust the BPM with F11/F12 (or Alt+F11 / Alt+F12) to get it more accurate. Also make sure to change the offset accordingly with I believe F9/F10.
OK now you have StepMania synced up to the song. But you still haven't cut out the middle parts you dont want. So in SM's edit mode, go to the measure where the section you want to cut out, begins. Somewhere on the screen you should see a "time" in the song at which this section begins; say, 45.108. Write this time down! That's how many seconds it is into the song where that section starts. Then go in SM's edit mode to where that section ends and write down that time as well.
Now open up the song again in Audacity and zoom in close until you reach this section. You can click on the waveform at the spot where the beginning of the section is, and then hold Shift and click on the waveform where the end of the section is -- this will *select* the section you would like to remove. Next, just press Delete and the section is removed. Now you can save the audio file and go back to SM's edit mode and see if it turned out nicely.
If you're really careful in Audacity, like to the millisecond, it should be almost seamless
Hope that helps; feel free to ask questions about it!