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 > Export from the menu in InDesign.
2. Export to a PDF (Print) format, a window for PDF settings presets will be shown.
3. Customize and save your settings with a label of 'edocbuilder' on this window and export.
After exporting the PDF this way, save the document, and upload it to eDocBuilder.
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.