We don't sync check numbers for Bill.com payments to your accounting software, however, you will see "Bill.com" in it's place. This will make it easy for you to identify which payments were made by Bill.com.
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.
Click Go;
The report shows all the individual payments grouped by day. In the Disbursement # field will be the check number;