This is a great question. Unfortunately, it is difficult to answer. It is an "impressionistic" autobiography, which means that if you don't take the details too seriously, there is a lot of truth packed into this important primary source: there can be a lot of truth in a lie! But there needs to be a deep level of source criticism if you are to try to take Twain for his word.

Even the title "Roughing IT" is a bit of farce: Samuel Clemens had grown up in a Mississippi mud hole, and although he had experienced something of Eastern metropolitan centers, his life in Virginia City and San Francisco exposed him to two of the most sophisticated, international, cosmopolitan urban centers of the nation. So he wasn't really roughing it, and I suspect he meant the title to be taken with a bit of the tongue in the cheek.

A specific example: Twain wrote about early Virginia City that

There were military companies, fire companies, brass bands, banks, hotels, theatres, "hurdy- gurdy houses," wide-open gambling palaces, political pow-wows, civic processions, street fights, murders, inquests, riots, a whiskey mill every fifteen steps, a Board of Aldermen, a Mayor, a City Surveyor, a City Engineer, a Chief of the Fire Department, with First, Second and Third Assistants, a Chief of Police, City Marshal and a large police force, two Boards of Mining Brokers, a dozen breweries and half a dozen jails and station-houses in full operation, and some talk of building a church.

Now this is a great description that ends with a wonderful punch line. Virginia City was founded after the big gold and silver strikes of 1859. It was incorporated as a city in 1861 and quickly became the largest city of western Utah Territory and then of the new Nevada Territory (organized in late 1861). Samuel Clemens arrived with his brother, who was to be the newly-appointed secretary-treasurer of Nevada. He started working in Virginia City as a reporter for the Territorial Enterprise newspaper in September 1862 (taking the penname "Mark Twain" in late February 1863). The earliest church was built there at least by 1861, and there were several religious institutions there by the time Clemens arrived. We can enjoy - and even use - his description of the diversity of early Virginia City, but we can't rely on all the specifics. And this means that unless you have the ability to "source out" each of his assertions, you really can't count on any of his assertions to be accurate. But the overall impression is accurate.

When it comes to his Western sojourn, there is, again, a lot of accurate details about the major events of his life. When we read Roughing It along side his collected letters, it is possible to understand some of what is accurate and what is not. The best thing to do is to read the authoritative material produced by Mark Twain Project of the Bancroft Library: its publications' notes help to sort out what is accurate and what is not, but each volume is large (and costly!). I find these sources to well worth it, however.

I hope this helps.