First, go to the "Settings > Save to > Metadata" tab. Inside of the "Tags" groupbox, there are various tag-related settings. To enable tag organization, check "Organize manga in folders based on tags". This will enable the "Tag Hierarchy" button, which opens the tag hierarchy editor.
If you start downloading before defining any rules, all downloads will go into an "Unsorted" folder. This folder is used for any content that can't be placed according to your hierarchy settings.
If you open up the tag hierarchy editor, you'll get a window that looks like this:
Let's say that we want to organize our content according to the "yaoi" and "yuri" tags-- "yaoi" content will go to the "yaoi" folder, and "yuri" content will go to the "yuri" folder. To accomplish this, simply add the two tags to the hierarchy by entering into the textbox at the top and pressing enter (or clicking Add):
The order is important! By default, tags will sorted alphabetically, and matched in the same order. If you download a manga that has the "yaoi" tag and the "yuri" tag, the "yaoi" tag will take priority, since it's listed first. But what if you don't want this?
You can control tag priority by specifying numbers inside of brackets to alter the ordering. To edit a tag, click it, and it will be loaded into the textbox again. To give the "yuri" tag priority, we can give it a priority number of 1, and the "yaoi" tag a priority number of 2:
Okay, so what if we want to refine our organization further? For example, what if after adding something to our "yuri" folder, we want to further divide it between "romance" and "mecha"? This can be accomplished by using subtags. To specify a subtag, add a new item to the tag hierarchy composed of the parent tag followed by the ">" symbol and then the child tag. You can chain together a virtually infinite number of tags in this fashion.
Consider the following:
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Yuri > Romance > Comedy
If we add another item to the tag hierarchy:
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Yuri > Mecha > Comedy
At this point, the contents of the tag hierarchy editor would look like this:
As you can see, it's not necessary to specify the tags individually (however, there's no harm in doing that if you choose to).
By default, the chain of tag folders generated will be suffixed to your folder formatting string. For example, if my folder formatting string is "[%STATUS%] %TITLE%", then the final path for the manga might be something like "Yuri\Romance\Comedy\[%STATUS%] %TITLE%".
You can override this behavior by using the %TAGSORT% token, which is replaced with the chain of directories starting and ending with a backslash. Maybe you want your content organized by status before tags-- In that case, you could use a folder formatting string like "[%STATUS%]%TAGSORT%%TITLE%".
Any questions? You're welcome to ask!