When I see a chronology where do I look to see how confident we are on those dates? Sometimes you only know that A occurs before B or that A occurs between two dates or on multiple conflicting dates. How then do you place A on a timeline and show it's uncertainty?

This is going to based on what kind of events you're portraying. There's no ISO 9000 for timelines, nor is there a general style guide. As with any visual representation of data (maps, graphs, charts, etc.), the one rule is that the reader can understand it easily. There's two solutions I would recommend:

Vague Scale: When doing long periods it's often could to use a rather broad scale like this. We might place the end of the "Maya period" at the fall of the last highland center, or the beginning of the Roman Empire at the start of August's rule, but where to we stick the start of the Maya and the end of the Empire? These are all debated topics with various, completely justifiable, date in use. If you round your dates to a large enough scale, though, you maintain an accurate, useful chart. You must be smart, of course, you can use a 20-year scale for polities/cultures of Mesoamerica or the Mediterranen, but even a scale of 1-year would just barely be enough for a timeline of emperors, what with Otho, Galba, Vitellus, and Vespasian and ruling for some months in AD 69. To further express uncertainty, I've also seen bars with faded/gradient edges to mark uncertain dates.
Event Boxes: You might be more interested in a chart like this. I've found this style to be the most adaptable. Use a time line with very few markings, and mark the date of events in the box. This lets you put things like "circa 1670" or "1678 (1680 in Other History)" or "1680 to 1691" all while maintaining relative chronology, if known.