Its package documentation gives information about \toprule, \midrule, \bottomrule, and \cmidrule, which is similar to \cline but also allows you to shorten the lines at their edges to put some small separation between midrules.
Historically, there have been conventions for making tables for publications that were put in place due to technological constraints, but now people still cling to them because they've grown up being used to those types of tables. booktabs makes it easier to make such tables in LaTeX. In particular, many people have (nearly religious) issues with vertical rules in tables, and so you need to provide your column separation in some other way. booktabs lets you make nice looking tables without vertical rues (or with vertical rules if you really wish).
You could put it before the tabular environment. Or if you just want to change the height of a single cell/line you could insert a \rule with a certain heigth but 0 width, invisible, into the cell.