Well brother that ain't very simple and I don't know if I can explain it in detail.
My methodology is as follows... READ
What do I mean by "read"? A lot of people go on blogs and websites and read random historical articles, for instance here's an article on Saqifah in which several researchers and narrations were quoted:
http://www.al-islam.org/restatement-history-islam-and-muslims-sayyid-ali-ashgar-razwy/critique-saqifaThis however my friend, is NOT reading. This is someone else doing the reading for you, quoting to you his own conclusion and expecting you to take it exactly as it is. This doesn't just apply to articles online but also contemporary books written by people who recently died, maybe a 100 years ago or so at least. Often times I read history books written by some contemporary scholar and I don't fully agree with a lot of what they say as it opposes my reading and research. When someone like Yasir Qadi offers a lecture on Karbala' and says "Mu`awiyah did this for this or that reason" I don't necessarily agree BECAUSE I READ and based on that reading I believe Mu`awiyah did the thing for a different purpose.
In other words, reading requires you to go back to the traditional classical historical sources yourself, the main history books that the nation relied on. When it comes to these sources, it is crucial to take into consideration a couple of matters, the earliness of the source and the earlier the better, the reliability of the author and his popularity and value, and the sources this historian relies on to present the historical material.
For example, we compare three historical sources:
"Al-Kamil fil-Tareekh" by ibn al-Atheer who died in 630AH, which is considered a bit late, this greatly reduces the value of the book when it comes to researching sensitive historical topics, the author is a renowned and reliable scholar but his book does not site its sources and chains, which is why when reading its contents I take them into consideration and benefit from them but cannot base my views on them except for what can be backed by sources from earlier books.
"Ansab-ul-Ashraf" by ِAhmad bin Yahya al-Baladhuri who died in 279AH which is very early, al-Dhahabi writes that he was writer, a historian, a poet. He is not known as a reliable scholar nor has anyone praised his Hadith, and even though he included chains in his book yet these to me cannot be accepted as authentic but are all historical stories that I take into consideration, if they agree with what is authentic or back it up I accept them as additional evidence, if not then I cannot build my historical view based on their content.
"Kitab al-Mihan" by abu al-`Arab al-Tamimi who is a Hafidh and a venerable Muhaddith, he died in 333AH which is not as early as Baladhuri but still very early, in his book he narrates with chains some of which are authentic and some are not. I would prefer this book the most out of the three.
So the above is simply an example and we can sum it up by saying, the you must always refer to the original resources and not take someone else's conclusions as fact. The researcher of history must have certain criteria as to what resources he must rely on, in this case keep in mind the earliness and popularity of the source, the reliability of the author and the availability and authenticity of the book's sources and chains.
Now when you do that and you wish to begin your reading, let's say you open Tareekh-ul-Tabari, the first thing you will notice is that each event is in its chapter and under each chapter are many narrations, some of these reports will be accurate, some will be partially accurate and others will be completely fabricated stories.
How do we figure out what actually happened then?
The first criteria is to draw a bold guideline, you do this by collecting the established historical facts that are authentic and popular. Anything which contradicts them is obviously an error and everything that agrees with them or backs them up can be accepted.
Unlike religious narrations, the historical narrations were not regarded as being so important that the scholars would go out of their way to find authentic chains for them, most historians exercise leniency in how they deal with such reports, this is why it is not very common to find solid authentic chains, you usually need to settle for acceptable chains most of the time.
For example, let's say we have a popular authentic report that says Abu Bakr sent three commanders to fight against the false-prophet Musaylamah and they defeated him.
Then you have two other narrations that are weak, and these two narrations actually announce the names of the commanders of of those three armies that Abu Bakr sent. We can simply accept these reports as they do not conflict or oppose the established authentic narration above, rather they back it up and provide more detail.
On the other hand if we find a weak narration that says that Abu Bakr only sent two commanders, then this is rejected as a historical error since it opposes the three narrations above, one of which is popular and authentic in chain.
Also another method of known what is accurate is simply to apply common sense and logic, for instance in the Shia book "Sulaym bin Qays" it says in one narration that Muhammad bin Abu Bakr was giving his father Abu Bakr advice while on his deathbed. We do not need to look into the chain of this report to know it is a lie, since it is established historically that Muhammad was around 2-3 years old when his father Abu Bakr died, so logically he can't have been giving him advice at that age.
Another way to know what is accurate and what isn't, is to dismiss what opposes what is known about a certain character. For example if we have a report in a history book that says "`Ali escaped with his life in Siffeen as he feared death." We know without checking this narration's chain that it is a lie because what is popularly known about `Ali in many other narrations and events both during the life of the Prophet (saw) and his own reign, that he was a strong warrior and he was very courageous, he'd never run away out of fear. Thus, these types of reports that oppose the Seerah of a certain person can easily be dismissed as historical errors.
At the end of the day though, the most important way is to analyse and authenticate the chain of a historical report. This is because many people could have lied in these past 1,400 years and if we do not have reliable narrators we cannot accept the report and this means the researcher needs to be familiar with historical chains, he must know the narrators and study their condition especially those who narrate a lot in history books such as Ibn `Uqdah al-Zaydi, Sayf ibn `Umar al-Tamimi, Muhammad bin `Umar al-Waqidi and many others. For example this is a study on the condition of a famous narrator in history called Ibn Lahee`ah:
http://forum.twelvershia.net/hadith-rijal/the-acceptable-hadeeth-of-ibn-laheeyah/One last thing I'll mention, is that historical reports are not like religious ones, in that when it comes to religious narrations if the chain is authentic you have to accept the entire text. On the other hand weak historical reports might have some parts that are accurate and other parts that are inaccurate, which means the historian who is narrating the story might narrate some aspects that are true and others which are not based on the information that reached him. When you read you'll find such reports and the well trained researcher will know how to dissect each historical report and differentiate between what is acceptable and what isn't.
^ Those are all some rough guidelines, when you dive into history and Hadith you'll know what we mean with practice.