First click on Local Servers in the Server Lists section on the left side of ConnectUO 2.0

Then above the server list itself, you will find a button that says "Add Local Server" Click this.

Next you should see the following screen:

Make sure you input a name, and valid IP address as well as the port for the connection.

If the server contains patches, make sure you right click the patches section of the screen and click Add Patch from the context menu.

Once your do this you should see a blank line, with a 1 in the version column. Double click the empty part of the line and type in the path to the patch

It should look something like this (Note: You may also use local paths like C:\patch.rar). Make sure you continue this process for each of the patches you have for the server.

Click OK and you should see the new server on the local serverlist.
If you change something in any of the patch archive files, you need to increase the version of the patch to let ConnectUO know it was updated so it may re-apply the patch.
To do this simply right click the patch you wish to update and click "Increase Version"

The patch should up the version, click OK to save this change.