The answer to your question is that as long as you match the color to the pin, it does not matter if the new arrangement is different from your old within that color group. The ATX 24 pin supply has 3 main voltages, 3.3 (orange), 5.0 (red), and 12 (yellow) all positive with respect to common (ground). Each derives from their own single rail. The other voltage to make sure you get right is the 5Vsb (standby), this line is always hot when the PSU mains are on, though the computer is powered off. The -5V is almost never used anymore, and I think the most recent revision (I would need to recheck) actually lists it as optional, the other is the -12 V line, don't get that one in the wrong spot either.
A PSU tester is always a good idea, even if the labels never fell off.
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