First create a new directory (folder) via FTP, something like /smiles
Log in to your ACP, expand "Smiles" on the navigation panel, click "Add New Smile"
In the right frame you will see two boxes, ignore the first one. The second Box "Add Multiple Smilies", is where you will be working.
Specify the category if applicable.
Specify the path (ex: /smilies), this is the folder you just uploaded > Press "Add Smilies"
You will then be directed to a page that shows all the smilies with the option of changing the bbcode (text replacement like :) = ), tick the box next to each smiley and hit add.
About category sorting: It would be wise to group your smilies in separate categories this way you can control how their are displayed on the post reply page, you don't want one large smiley to blow out your margins.
Make bulk additions easier in the future by creating 1 folder for smilies and then sub folders for each set. This way when you add new ones, you can just upload a new sub folder and not worry about trying to importing the same smiles twice, which will cause errors and frustration on your part.