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Timer0 will keep varying each time you reset, and there's no real way to control which value it takes. Thankfully it'll only take a certain number of values, and some of those should be more common than others. This is why you calibrate a number of times - to work out which range of values is most common for your DS+cart combination.
I'd suggest repeating the calibration step about 15-20 times, or until you can see one or two values being significantly more common than others. Use that range in your RNG Reporter profile to search over those values in future.
Timer0 will still vary when you go to the main RNG process and want to hit a specific seed. But by knowing which timer0 values your game picks most often, you can use those values to find seeds you're more likely to hit quickly.
The timer0 is what you mainly need to calibrate your RNG Reporter to give you the correct seeds. The seed should be the same if you're hitting the same one, but what you want is the timer0. If you're doing BW1, it's likely you'll hit the same one pretty quickly, but I personally had to do the timer0 in BW2 around 40-50 times before I concluded which timer0s I was most likely to hit.
Calibrate > timer0 & other settings (saved to a profile) > set IVs/nature > generate seed with profile > get initial frame > use save positions or chatots to advance frame to desired seed (may have to be done many times due to timer0 fluctuation).
For calibration, the seed isn't important. Getting the same seed just confirms that you're doing the process correctly, even though the timer0 fluctuates. What's important is determining what timer0 is most common, and using that to set the profile. As the timer0 can be a bit hard to pin down, it's important to do this quite a few times, as choosing a timer0 that only appears 1/10 is going to cause you heartache when RNGing.
Once you're calibrated, and the RNG Reporter can use your cart/DS settings as inputs, you're then able to generate the seed which will result in your desired Pokemon. That's when the seed is important. :)
The seed will give you the correct time and frame. It's important to get both of those elements right. Because of the timer0, if you are playing BW2, you may have to restart many times to get the correct timer0, on the correct time with the correct frame.
The seed is only used as an index to that particular frame, in relation to your cart. The actual hex value is not important until you are using it to generate the research seed table (for timer positions) or retrieve that data again.
Just think as the seed as a reference or a bookmark to those particular stats that will be generated with those specific inputs (time, frame, keypresses).