Is it possible directly talk to the seriel ports on the Seeeduino Mega, over usb, using the FTDI chip?
I don't think your question is clear enough for a good answer.
The first serial port on a Arduino mega already wires directly to a on board USB FTDI serial convertor chip. It appears on the PC as a simple comm port. The other three Mega serial ports use TTL voltage levels and requires a MAX232 type voltage translator chip to communicate directly to RS-232 links. The mega serial links can wire directly to external serial links if they use TTL voltage levels.
So what external device are you wanting to communicate with (and what voltage levels does it use) and which Arduino serial port number are you considering using?