First Download http://www.ftdichip.com/Support/Utilities/FT_Prog_v126.96.36.199.zip
Click: Devices/Scan and Parse and after you made you changes: Devices/Program
By default the USB-host max allowed current is set to 90 mAmp, change it to 500 mAmp.
When you power your board trough a USB Charger it will of course not enumerate and the ftdi chip will never set PWREN# low and you will get no juice.
Change C3 to be BitBang RDn and it will stay low and you get power with both USB host and USB charger.
Some special chargers have minimum current or it will shut off, so test different onces.
Using Bitbang WRn will always stay high for then you never want to use USB-host power, useful if external 1amp power is used and usbport is only used for rx/tx debug etc.
You can also do the above functions in jumper settings on the Quickstart board or on your own add-on board.
Connect a 0-1k resistor between 6th pin from the right to gnd for always power on or 0ohm jumper to Vin for always off.