The answer depends on the type of template you are referring to - Standard Forms or interactive designer. In both instances you would set your master PDF to a size that accommodates the bleed. For example, if you want your final piece to be 3.5" x 2" and you set your bleed to be .125", then your master PDF should be 3.75" x 2.25". You would not set any bleed in your master PDF. After uploading your master PDF into the template in eDocBuilder, you would set the bleed on the Template Info tab in eDocBuilder. The way this bleed is displayed differs depending upon the template type:
Standard Forms Based Templates
The preview displayed to the user reflects the final product with the bleed removed. There are no user interface elements on the template that indicate bleed for user as they cannot move design elements outside the bleed area.
Interactive Designer Templates
Notice on the preview pane when customizing the template that there are two dotted lines - one is red and the other is grey or white. The red line on the template represents the bleed. The white or gray line is a "safe zone." This line is meant to indicate to the user that any text or images beyond this line are going to be close to the cutting line. The width of both lines will be the same.
For example, if you set a 9 point bleed in the template info tab, you will see the red dashed line at 9 points and the white or gray line at 18 points. Neither of these lines will prevent the user from adding text or images outside of the bleed or safe zone. Please see this screen shot for further explanation:
But what about PDF's?
There are several kinds of PDF's that are generated by eDocBuilder, but none of them will indicate the difference between the bleed and non-bleed parts of the page. Whether you're looking at a proof PDF, "allvdpproof.pdf", or the production PDF, they all will indicate the full bleed width of the page.