If you went around to researchers and asked them this question, I suspect you'd get a different answer for each one. Here are some of your options for recording genealogical information:
- paper systems designed for genealogy research, such as the forms in the workbook accompanying Emily Anne Croom's book Unpuzzling Your Past
- software made specifically for 'doing genealogy' (more on this below)
- keeping your findings in narrative format in a research journal and your search results in software made for general office work (Word / Excel / editor of choice), notekeeping (OneNote/Evernote) or writing (Scrivener)
One problem with using software designed for "doing genealogy" is that most people are only familiar with the lineage-linked genealogy software which based on GEDCOM, a standard created by the LDS Church to communicate data about the lineages we think we know.
In my opinion, lineage-linked software is not well-suited to the task of managing information while we are still in the process of figuring stuff out -- it is focused on keeping track of people, when what the researcher is doing is collecting and analyzing records about people. It is good for recording 'conclusions' -- or if you don't like that term, you can substitute 'theory' or 'your best guess about what's true' -- but not necessarily for Managing the Multiple Maybes.
See What tools exist for collecting and managing evidence? and Transitioning from person-based genealogy to record-based genealogy? for previous questions and answers that touch on this problem.
As people become more familiar with modern standards for doing genealogical research such as the Genealogical Proof Standard, more source-centric software and evidence-management tools are becoming available to us, such as:
- Lineascope, an online browser-based application that aids the user in analyzing information in sources, and preserving the analysis for use in a proof statement
- Evidentia, software that supports the user as they go through the analysis of a source (walking you through the process used in the Genealogical Proof Standard)
- Clooz, software which is designed to help the user inventory and analyze documents and other source material
- Custodian, designed for people doing large one-name and one-place studies -- it helps "store, index and organize the information" collected for the study
But the best way to answer the question of "what do serious folk do" is to look at the actual work product of accredited and certified genealogists. If you are at RootsTech, NGS, or other large genealogy conferences, look for booths run by the Board for Certification of Genealogists (BCG) or the Association of Professional Genealogists (APG) to see if they have sample portfolios you can examine.
On the web, the BCG offers work samples on their website. Elizabeth Shown Mills, the author of Evidence Explained, offers a series of QuickLessons including QuickLesson 20: Research Reports for Research Success -- the notes in that quicklesson have links to her website Historic Pathways where she generously shares copies of publications and work samples.
Another thing that helps us get better at analyzing records is to learn more about how the records were created by reading journal articles like Claire Prechtel-Kluskens' Who Talked to the Census Taker?, the instructions given out by the agencies at the time the records were created, or the reference information papers and finding aids created by the archivists who have custody of the records now.
Taking your example:
the family folklore/history says he was born in Brooklyn Iowa in 1860.
The US Census records of 1890 and 1910 say he was born in Illinois.
One Census record shows the family name as spelled Ferrell (two E's).
Another record shows him as being born in St Louis MO.
What we all need to do, and often fail at, is to write down why it is that we thought these records belonged to our person, despite the fact that they don't agree with our family stories.
Whatever method you choose to keep track of your research process, until you are comfortable with the concepts in the The Evidence Analysis Process Map, the best thing to do is write your analysis out explicitly, so you can go back later and see what you've done. Even if we don't want to create formal research reports and proof statements for publication, it's still helpful to write these things out for ourselves -- it makes it easier to go back to a problem later and pick up where we left off.
Whether you keep the information in a separate program like Word of Scrivener, or write research notes that get attached to specific people in your lineage-linked software, or something else, write everything out explicitly so it will be easier to review later.
A narrative in a plain text file has the advantage of being easier to access by multiple programs and operating systems. I use Scrivener for a lot of my research notes because the files are stored in Rich Text Format rather than a proprietary format, and can be read independently outside of Scrivener's environment.