John, scholars are able to determine these things via textual criticism because it is a science. There is a very particular way to go about doing it which takes all sorts of things into account.
Let me give you one example of how this sort of thing might work. One of the reasons that manuscripts become different is because of the way copies were made. If a manuscript of Mark in one city were to be copied and a mistake was made, then other manuscripts copied from that one would include that mistake. However, this particular mistake would be limited to those manuscripts made in that city. Eventually, this mistake would move elsewhere as manuscripts from that city were brought to others, but in ancient times these cases would be relatively negligible.
Now, in another city, a different mistake may be made, and the same sort of magnification would occur as manuscripts were copied. Going forward two thousand years, its not overly complicated to look at the grand total of manuscripts available and figure out what was there in the first place. If a mistake was made copying the manuscript in Alexandria, it may spread elsewhere, but by and large that particular mistake is going to be very uncommon in the broader world. So, if we see a paricular difference occuring primarily in Alexandrian manuscripts, its fairly accurate to say that that is probably a mistake made in Alexandria, because otherwise it would be more widespread.
On top of this general principle, we can look at the dates of manuscripts and determine that a particular variance never occured until x AD. In that case, it’s again fairly accurate to believe that that was a mistake that was not in the original.
Then there is other evidence that can be found. Sometimes, there are fairly thorough records as to where a manuscript came from, and this can help. Other times, there are less thorough records or none at all. All of this evidence can help.
In terms of the time frame, the oldest manuscripts are generally preferred. Unless there is some reason to think otherwise, the best way to get what the original author wrote is to find the oldest manuscript. That really is what we are after - what the original author wrote. Thus, the oldest manuscripts make sense.
The important thing to realize in all of this is that very rarely do any of the variances effect doctrine. Having been involved in apologetics pretty deeply, I can attest to the fact that the most controversial of all differences in the Scriptures are over minor things that don’t make that much of a difference. The biggest question I can think of off the top of my head is whether St. Paul wrote “we have peace” or “let us have peace” in Romans 5:1. It’s somewhat important, but not really, and it doesn’t effect anything that can’t be worked out with countless other passages.
Also, despite what John mentioned about in Tobit, the vast majority of cases where there is any difference are noted in the footnotes of your Bible.
Of course, some Bibles are better than others at this.
There’s no need to doubt your Bibles, though. This is why we read them for enlightenment, use them to learn doctrine, ought to have a few translations for when we want to really get into a particular passage deeply, and ultimately rely on the Church that God gave us so we don’t have to worry about things like this unless we want to.
