Can I customize the automatic billing rules and filters for eBay transactions?

You can set configurations for automatic e waybill generation in BUSY as per followig steps
Step 1: First you have to create a GSP (GST Suvidha Provider), you need to visit the eway bill portal. 
Step 2: Select Webtel Electrosoft Private Limited and Pinnacle Finserv Advisors Private Limited as the GSP Vendor type.
Step 3: Go to Administration and click on configuration.
Step 4: Select Features / Options and click on GST / VAT, here you will see a option called E-Way Bill Required.
Step 5: Set Y to turn it on and mention your place and pincode,you can also mention amount after which ewaybill is to be generated for local as well as central transactions with user restrictions also and GSP username and password in GSP Configuration tab and save the configuration
Step 6: Go back to Administration and click on configuration.
Step 7: Choose the Voucher Series Configuration option and select the voucher type for which you want to generate e invoice, such as sales, sales return, etc.
Step 8: Then, select the voucher series and click on Voucher Configuration.
Step 9: Here, you will see options of Input Transport Details, Generate E-way bill After Saving, set Y to enable that. 
Step 10: Now when create invoice can generate automatic e-way bill.