According to IRS Publication 521, "Expenses of entering into or breaking a lease" are not deductible moving expenses.
There is no way to allocate the $1000 to the nondeductible expense of breaking a lease. The IRS only considers deductible moving expenses, and those expenses have to be reduced by any reimbursements received. Any nondeductible expenses are considered personal expenses that the IRS does not take into consideration.
How you account for the reimbursement from your employer depends on whether the payment was part of an "accountable plan." If your employer does not have an accountable plan, the $1,000 is fully taxable and included in box 1 of your W-2. In that case, the payment is not a reimbursement under moving expenses. However, if the relocation assistance was given to you under an accountable plan and not included in your wages, then it is non-taxable and has to be reported against your deductible moving expenses.
In the end, allocating the assistance payment to a particular expense is not a relevant approach. What matters is (a) the total dollar amount of deductible moving expenses, and (b) the tax treatment of the $1,000 payment from your employer.
Please review IRS Pub 521 for more information on deducting moving expenses.
https://www.irs.gov/pub/irs-pdf/p521.pdf
