Presumably you want the one connected to your displays to be "(1)" and the other to be "(2)"? Devices are enumerated automatically and that screen isn't meant to imply any order of installation. The "order" doesn't really matter anyway. SLI will take care of everything regardless of which order the GPUs are enumerated.
The only time this ever becomes an issue (IMO) is if one card is getting really hot. Then you have to pay attention to this as it can tell you which card has a cooling problem. Note that usually one card will be slightly warmer as the load isn't split perfectly. It's really only reason for concern is if one card is getting substantially hotter so that it's throttling.
If you're having problems with PrecisionX it's likely unrelated. That software shouldn't care what order the cards are installed either.
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