Do you mean positioning the image and knowing where the hole will be?
I've found a simple solution to that, made possible because GIMP is a serious image-editing program that supports layers. I have a template with a separate layer that has white painted in the areas that are "void" - i.e. the central hole and the area outside the circular CD area. All my image-messing-about is done on other layers. I make this "guide" layer invisible before collapsing all the layers into a single image, saving as JPG and importing into the CD-labelprinting software.
My template is for GIMP (it's an .xcf file), and is designed for the Verbatim printable discs I used (central hole diameter 260mm, outer diameter 118.4mm); I'd be happy to send it to you or upload it here if there's an area for that.