Make sure you understand the difference between improvements and repairs.

An improvement adds to the value of your property, prolongs its useful life, or adapts it to new uses. Examples of improvements include paving a driveway, adding a bathroom, and replacing a roof.

A repair keeps your property in good operating condition. A repair does not materially add to the value of your property or substantially prolong its life. Examples of repairs include fixing a leak, replacing broken windows, painting, and repairing a roof. You deduct the cost of the repair as a rental expense.

If you improve or make additions to a rental property, you must treat the improvement or addition as a separate depreciable property. The improvement or addition must be depreciated over its useful life and cannot be deducted in the year paid.

You should check with your tax advisor to be sure, but if this is a capital improvement you should add a Fixed Asset account to your chart of accounts (Lists – Chart of Accounts) and then book the bill or check to the balance sheet account you created. In order to track the payment for 1099 purposes, you'll also need to include the new account in your 1099 mapping (Edit – Preferences – Tax: 1099 – Company Preferences) and make sure you checked the "Vendor eligible for 1099" box on the Additional Information tab on the vendor record.