So, you've bought O365 for your enterprise environment, congratulations!
As part of the installation process, the user is expected to run the O365 Desktop Setup tool. This tool configures the desktop to use O365. What does this mean?
Well we need to setup Lync, Sharepoint and Exchange to work with your desktop. The desktop setup tool configures registry and other bits of information to work with the O365 environment. This is particulary important if you are coming from an on-premise Lync / OCS or BPOS environment.
There are some registry settings specific to the MOC which will cause weird results with a Lync client. The weird results are some prompts for usernames and passwords as well as some slowdown during login.
The only issue with desktop setup tool is that you will have to download and run it to every user machine. Not so bad if you only have 5 or 6 machines, but can be painful rolling it out to 60,000 + seats.
So there is a manual way around this tool, have a look here http://onlinehelp.microsoft.com/en-us/office365-enterprises/ff637585.aspx. Specifically for Lync online:
So there you go, the easy way NOT to have to run the O365 Desktop Setup for many many users.
Of course, running it is much more preferable, if you can't though, I'm sure you can get an admin script or GPO to edit the required registry for you.
If you are coming at it fresh, i.e. the machine you are installing on didn't have Lync or MOC installed, you can simply run the Lync client and all will be set up for you.