QB Issue Resolution:

No. Bonuses should be added to paychecks as a type of taxable earnings item. QB has an item just for this, of the type Bonus.

Resolution for Issue 'Do I have to include year end bonus on 1099 for employees?' available: Yes (Solved).
Source: Intuit Community forum.

Do I have to include year end bonus on 1099 for employees?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for 1099
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Error Recovery for 1099 [Canada]
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