There is a video on using sweaver with the omega theme. As you used the omega theme explicitly I got the imagination that there are special features in omega and/or sweaver to cooperate. But you could have used any other theme, too :(
What about a real integration with sweaver and omega or delta: add the css files created with sweaver to the list of switchable css in the omega/delta settings (as you can with css-files provided by the modules). This could be done on the sweaver UI when saving a css-file: add a check box to register the css-file with omega (unless omega is installed, of course).