Do I need to set-up my artwork file differently for different colors of Tote Bags?

No. For all Tote Bags; the background color of your artwork must be transparent if you want the color of the bag to show. Saving a transparent PDF or TIF file is the best way to do this. You can also send in EPS files with no background. For example, if you want a logo printed on a bag and your artwork contains the logo with a white background, or any background color, it will print as you see it on the file. The logo must be on a transparent background if you only want the logo to print.