Must I set the time zone in the polling configuration to match the time zone of the Quickbooks server?

Yes, the timezone in your polling configuration should match the timezone of your on-premise server where Quickbooks resides. If you use the default polling, it will use UTC time and this can cause missed events if the time comparisons are off. It is also recommended that you use a format that does not require updates for Daylight Savings time.

The following json snippet is an example of the correct poller configuration with a Mountain Time: 

{
"payments": {
  "url": "/hubs/finance/payments?where=TimeModified >= '${dateTimeZone:America/Denver:yyyy-MM-dd'T'HH:mm:ss.SSS'Z'}'",
  "idField": "TxnID",
  "datesConfiguration": {
    "updatedDateField": "TimeModified",
    "updatedDateFormat": "yyyy-MM-dd'T'HH:mm:ssXXX",
    "createdDateField": "TimeCreated",
    "createdDateFormat": "yyyy-MM-dd'T'HH:mm:ssXXX"
     }
  }
}