If you are starting from nothing (no existing git or git-annex repository) and want to use a server as a centralised repository, try the following steps.

On the server where you'll hold the "master" repository:

server$ cd /one/git
server$ mkdir m
server$ cd m
server$ git init --bare
Initialized empty Git repository in /one/git/m/
server$ git annex init origin
init origin ok

Clone that to the laptop:

laptop$ cd /other
laptop$ git clone ssh://server//one/git/m
Cloning into 'm'...
remote: Counting objects: 5, done.        
remote: Compressing objects: 100% (3/3), done.        
remote: Total 5 (delta 0), reused 0 (delta 0)        
Receiving objects: 100% (5/5), done.
warning: remote HEAD refers to nonexistent ref, unable to checkout.

laptop$ cd m
laptop$ git annex init laptop
init laptop ok

Add some content:

laptop$ git annex addurl http://kitenet.net/~joey/screencasts/git-annex_coding_in_haskell.ogg
addurl kitenet.net_~joey_screencasts_git-annex_coding_in_haskell.ogg (downloading http://kitenet.net/~joey/screencasts/git-annex_coding_in_haskell.ogg ...) --2011-12-15 08:13:10--  http://kitenet.net/~joey/screencasts/git-annex_coding_in_haskell.ogg
Resolving kitenet.net (kitenet.net)... 2001:41c8:125:49::10,
Connecting to kitenet.net (kitenet.net)|2001:41c8:125:49::10|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 39362757 (38M) [audio/ogg]
Saving to: `/other/m/.git/annex/tmp/URL--http&c%%kitenet.net%~joey%screencasts%git-annex_coding_in_haskell.ogg'

100%[======================================>] 39,362,757  2.31M/s   in 17s     

2011-12-15 08:13:27 (2.21 MB/s) - `/other/m/.git/annex/tmp/URL--http&c%%kitenet.net%~joey%screencasts%git-annex_coding_in_haskell.ogg' saved [39362757/39362757]

(checksum...) ok
(Recording state in git...)

Don't forget to commit it:

laptop$ git commit -m 'See Joey play.'
[master (root-commit) 106e923] See Joey play.
 1 files changed, 1 insertions(+), 0 deletions(-)
  create mode 120000 kitenet.net_~joey_screencasts_git-annex_coding_in_haskell.ogg

All fine, now push it back to the centralised master:

laptop$ git push origin master
Counting objects: 20, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (11/11), done.
Writing objects: 100% (18/18), 1.50 KiB, done.
Total 18 (delta 1), reused 1 (delta 0)
To ssh://server//one/git/m
   3ba1386..ad3bc9e  git-annex -> git-annex

You'll probably want to use git annex copy --to origin to copy the annexed file contents to the server. See the walkthrough for details.

You can add more "client" repositories by following the laptop sequence of operations.