Hi Chris,
I'm not sure if I understand your question but correct me if I'm wrong. When dealing with a clock signal, you can only have 1 source. There is no way to "multiplex" the RTSI lines together to increase the scan rate. So you would have to choose 1 line or the other.
In terms of using the Select Signals Express VI, this is a software signal selector. This VI can not control the hardware signals on the board. The idea behind this VI is that if you have multiple signals coming from a software read, you can use this Express VI to select a subset of these signals. This function is purely selecting signals in software and not the hardware of the board.
I hope that clears things up. Have a good day.
Ron