Generally, multiple single letter flags can be combined into a single argument. In this case:
cp -ar ../foo/bar/. qux/quux/
is equivalent to:
cp -a -r ../foo/bar/. qux/quux/
If you look in the manual, it will tell you that -a is "same as -dR --preserve=all". You can look all of those up if you want, but the short version is that the -a flag causes the new files to have the same permissions, owner, timestamp, etc. as the original files. (Normally, they would be owned by the user performing the 'cp' with permissions defined by your shell configuration, and a current timestamp.)