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Unless you know what you're doing, do not do anything manually on the server (except when the documentation says you should, for example to add custom hooks). In particular, adding new repositories or users or changing the access control rules should not be done directly on the server. Things will break. For example, if you manually create a repo on the server, it will not have the required "update" hook, without which there is no access control for pushes.
Most normal (day-to-day) gitolite admin work is done by cloning the gitolite-admin repo from the server to your workstation, making changes to the clone, and pushing those changes back.
The installation steps in the previous section include the steps to do this
clone, so you should already have one on your workstation, in
~/gitolite-admin. You can of course clone it anywhere else you want and use
that clone.
Either way, make sure you cd into this clone first.
Note: some of the paths in this document use variable names. Just refer to
~/.gitolite.rc for the correct values for your installation.
Once you've cloned it, you're ready to add users and repos.
The custom hooks feature is a blunt instrument -- all repos get the hook you specified and will run it. You can of course install hooks manually on the server, but sometimes that's cumbersome.
Instead, you could set your hooks to only work if a certain "gitconfig" variable was set. See this for a way to specify "git config" settings on a per repository basis.