Hafidz,
I strongly urge you to consider some SCXI multiplexing or other multiplexing hardware. The time and energy you expend writing equivalent software will be more of a price than you will want to pay. Unless you are in a financial fix, and can just throw a programmer at the problem (which costs MUCH more than hardware by the way), you should consider the hardware.
If you need to use software, you should try to get in some kind of timing signal in order to synchronize the signal. If it were me, I would simply send a digital pulse in conjunction with one of your signals to another analog line, and use that to determine where you were in the data.
Hope that helps.