A common way to read from multiple file descriptors in linux is to use select(). I suggest starting with the manpage. The basic system flow is as follows:
1) Initialize devices
2) Obtain list of device file descriptors
3) Setup the time out
4) Call select with file descriptors and timeout as parameters - it will block until there is data on one of the file descriptors or the time out is reached
5) Determine why select returned and act accordingly (i.e. call read() on the file descriptor that has data). You may need to internally buffer the result of read until an entire data gram is obtained.
6) loop back to 4.
This can become your programs main loop. If you already have a different main loop you, can run the above without looping, but your will need to insure that the function is called frequently enough such that you do not lose data on the serial ports. You should also insure that your update rate (i.e. 1/timeout) is fast enough for your primary task.
Select can operate on any file descriptor such network sockets and anything else that exposes an interface through a file descriptor.