You can get a list of check numbers for your Bill.com payments by running a Funds Transfer Detail Report:
In Bill.com, click the Reports tab, and under Payables Reports click Funds Transfer Detail for Bill.com Payments.
When the Funds Transfer Detail page displays, enter a date or date range; group the results by date or vendor; and select a Report Format.
The report shows all the individual payments grouped by day. In the Disbursement # field will be the check number;