Monitoring two serial lines at the same time
If you're on a 32bit Windows OS, I would recommend using PortMon.  It goes down to the millisecond at least.  It might even be microsecond resolution.  I've used it a lot in the past with great success.

In your particular case, you will put each FTDI chip on its own serial port.  Then in PortMon, simply select the ports you want to monitor from the pulldown menu.  Both sets of data get logged at high resolution, and you can even add filters to reduce the amount of data.  For serial protocol monitoring, I add the include filter IRP_MJ*.