Paying a contractor who also owes us money

How did you enter the cost of the ticket when you purchased it?

When I pay our contractors, I create a bill that sometimes has multiple line entries.  Most of the entries have a category that has something to do with Subcontractor expenses - and for the description I enter information about the job they did that I'm paying them for. 

If it were me and when I purchased the ticket for her I entered that transaction in QuickBooks with a category of "travel", I would create a bill that has:

• a line for each of her stipends and reimbursements with appropriate categories, descriptions and amounts
• I would add another line with 
  • category of "travel",
  • description of "repayment of airline ticket for spouse - Prior Balance: $$$, Balance after this payment is applied:  $$$
  • amount: negative of (the smaller of the total of the income lines on the bill or the amount she still owes you).

Alternatively, instead of a category like "travel" when the ticket was purchased, you could create a new "asset" in the chart of accounts that is something like "Loan to Employee X".  Then that asset would be used as the category for both the ticket purchase and the repayment listed on the bills.  When that asset goes to zero, her debt is repaid.