No noticeable lag.
Sata is a point to point architecture. When B is transferring data on the bus, there might be some minimal interference. But the maximum hard drive data transfer rates are half the capability of sata2. If your external drive is usb, it can recieve data at a much lower rate, minimizing the interference even more.
Lastly, the OS on drive A does mostly small random reads and writes which take up little of the bandwidth.
---------bottom line------------ not to worry.