Alias "/someDir" "/webSiteDir"
Alias "/anotherDir" "/var/www/html/thisDir"
Alias does not care much about your documentroot in a sense. That is, just define Alias inside your VirtualHost, first argument is a new virtual path and second is always a filesystem path, can be or it can not be inside the documentroot, Alias does not care or differentiate about it.
So, to question 1.
Always use alias to define virtualpaths, irrespectively where the filesystem is, just use it when you need it.
To question 2.
You have a BIG misunderstanding, Directory ALWAYS specifies a full path in your OS, that is
<Directory "/">is / in your OS Filesystem and the same with the rest of your "Directory" examples.
If you wanted to affect a path created with Alias, you would use "Location" or Directory with the full path, and that one is really relative to documentroot.