When exporting an indesign file as an eps sometimes around a circular logo the background area will stay white behind it, so when put against a colored background it will show up white behind the logo instead of the color of the background. How do I fix this? And can I fix this in the indesign file so it won't occur evertime I eps this file or do I need to fix this everytime in the eps file?
Moved from the Creative Cloud to the InDesign forum. They will be able to help you here.
First question is why are you exporting to .eps from ID?
Second question, is the background a spot color?
.eps doesn't support transparency, so if you have a transparent logo it needs to get flattened. When you export to PDF with flattening, you can Simulate Overprint (see InDesignSecrets » Blog Archive » Eliminating the White Box Effect) but that's not an option for .eps. You probably need to add a clipping path.
There is no good reason I can think of to export InDesign to EPS. Last I heard, it was used by some backward-looking printers who still placed InDesign files in QuarkXPress. You lose almost everything placing in the format. Not only transparency but metadata, color management, accessibility, editability, etc.