FTDI/MCU design question to detect boot mode
I recommend you verify with FTDI datasheet as well as their support pages (they have a decent knowledge base).  I have done a similar design:

You can use any of the CBUS pins of the FT232 to connect to the nBootmode pin of your chip.  If the signal is the wrong way, then you can program the FT232 EEPROM to invert it.  This means as FT232 powers up, it'll set those pins.  You might want to employ a similar thing with nReset of your MCU, that way it'll remain in reset mode until FT232 is up and ready.

You'll likely need to manage separating the power bus using diodes such as a BAT54C or schottky diodes likes this: 
 

Think about what would happen if both power ports are [accidentally] plugged in.  

Regarding the PWREN#.  It is meant for shutting down power of an external chip during USB suspend.  It might be tricky in this case since it is low during USB enum, but it only goes high again during USB suspend which might prevent you from interacting with MCU.  You might want use a generic CBUS IO and flick it up or down using the driver or one of the UART lines, etc.

Finally, most FT232 chips can't supply more than 50mA of current.  Check that your MCU power requirement is lower.