The new version of the eDocBuilder Plugin for Adobe InDesign supports using preset settings saved in the PDF export settings for that document.
1. With your document open, go to File > Adobe PDF Presets > Define
2. Click New, a window for PDF settings presets will be shown.
3. Customize and save your settings with a label of 'edocbuilder' on this window and click OK
4. Click Done on Adobe PDF Presets Window
Before this current version of the plugin, there was no way to reference these settings other than doing an export from the current document to set them, prior to uploading the template to eDocBuilder.