We have a battery powered device. We need to shut down as much of the device as possible when not active. We are connected to a Bluetooth device through a UART and we want to manually set the RTS line to the proper state then place the UART in low power mode/turn off and go to sleep.If data is received into the Bluetooth device, the device will set a wakeup pin to the SOC and wake the device from deep sleep. I need to know how I can manually set the RTS state before going to deep sleep or does the Power Management framework take care of this automatically.

We would need to know the hardware & software. In the old days, everything was accessible; Now, RS-232 protocols are implemented in some tiny corner of a massive asic, or maybe an rs-232 chip (e.g. MAX232)is soldered in, because rs-232 is funny with voltages (+/-5V iirc).
The bluetooth device muddies the waters considerably. It is unlikely you will find too much of that is accessible, as rs-232 is usually just 3 lines, send, receive & earth. You should be able to disconnect RTS, and it should work. Any rs-232 or power saving implementation requiring a particular state on an (almost obsolete) RTS line is strange.