Why does MSP430 have 2 capture signals for each capture/compare channel? Pin assignments recommendations?
It's just extra flexibility. TI goes to extremes when it comes to alternate functions for a single pin. Some pins on the MSP430G2553 have as many as 9 alternate functions. This is a part of the Timer_A diagram from the MSP430x2xx Family User's Guide (p. 365):  



The CCISx select bits allow you to switch between two different timer capture signals.