We’ve just rolled out an update to allow EPS file upload via Magento. No change is needed to the Magento end.
Possible issues with EPS files
Some EPS files cannot be processed. Please, email them to us for analysis.
You need to make sure that your server has the right MIME type set up for EPS files. Contact your system administrator or the hosting support if the MIME type is not set. It should be application/postscript.