If you have not already done so, configure the AirPort Base Station not connected to the router to "extend" the wireless network created by the other AirPort Base Station. Read this for a more thorough explanation:
Take note of the following in the above, which I recommend:
If you have configured your Wi-Fi base stations in the past, it may be helpful to do a factory default reset of each Wi-Fi base station that will be part of the wireless extended network before you begin.
As well as the following:
The physical location of extended Wi-Fi base stations will vary according to the building environment and may require some experimentation.
If feasible for your installation, a "roaming network" is the ideal configuration, and precludes the need for experimentation.