QB Issue Resolution:

One option would be to use the “Bonus” feature, and use $10,000 and $20,000 as the amounts. You can then manually calculate the Federal Income Tax withholding amount based on an “Annual” payment period using the tables in this publication, and override the amount the QB calculates.
http://www.irs.gov/pub/irs-pdf/p15.pdf

Resolution for Issue 'We are a new non-profit, and we owe two employees for 2013 pay and 2014 pay. We want to pay them their annual amount in one lump sum ($10K and $20K respectively).' available: Yes (Solved).
Source: Intuit Community forum.

We are a new non-profit, and we owe two employees for 2013 pay and 2014 pay. We want to pay them their annual amount in one lump sum ($10K and $20K respectively).: 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.

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