If you pay a vendor, and they are eligible for a 1099, then all payments are reported.
No you can not mark one payment as not for a 1099 when it hits the mapped expense account. post it to a different expense account
but
trying to reimburse expenses to a vendor is dicey, if you get the original receipts for the expense, then you have documentation for the expense, but if he keeps them he may also deduct that expense, which would be wrong.
he is in business and has expenses and income, he should invoice you his customer for his expenses, service and markup, then you pay him, that is his income.
