Hi,
If you want to download application code to on-chip flash of LPC1769, it is okay to use Flashmagic tools to download *.bin in ISP mode.
1)after Reset, the P2.10 pin must be low so that the LPC can enter ISP mode, after you have downloaded the application code, then you have to configure the P2.10 high so that the application code can be executed.
2)you have to use uart0 pin, in detail, P0.2 is TXD0 pin of uart0, the P0.3 is RXD pin of uart0, the two pins must be connected to the FTDI usb2uart converter.

Pls check if you have connected to uart0 to the FTDI and if the USB can be detected by PC with a virtual port.
Hope it can help you
BR
XiangJun Rong