Rails are independent power channels.
For example:
Rail 1 5 Volt 20 Amp
Rail 2 5 Volt 30 Amp
You have a total of 50 Amp at 5 volt, but they are isolated.
Positives:
A electrical short on 1 rail will not effect the other rail and vice versa.
Negative:
A device requiring 35 Amps at 5 volts can not be connected since neither rail has that much.
Video cards are generally placed on a separate rail, whenever possible, since they consume so much power.
The same principles apply for 3.3V and 12V.
If any rail drops below 5% of the stated voltage you need to move something to a different rail. 5 volt can go to 4.75, and 12V can go as low as 11.4V (but should not)
You need to check the rails under load and not under idle.