[Zalbag]

I have several questions concerning Calibre so I’ll try to group them properly.

How do you embed the metadata to your original files? As in, overwriting your original metadata for your files. I couldn’t find that option but, I can only assume it’s under Preferences: Import/Export: Saving Books to disk?
Meta Data Questions: Under, Preferences: Sharing: Metadata download: What websites should I set to priority and can I input additional websites to search from into Calibre? Also, why do multiple websites have their priority set to 1 or 2 instead of in a sequence?

If I can’t find the metadata for the books or it returns with the improper information how can I crop the image from the pdf/epub file and set it as my cover? If it has the right cover and information concerning the title, author & etc will that help it find the metadata better? I’ve tested Calibre’s metadata search and it seems to have problems with finding light novels, some comic books and the right manga volume #’s. Are there sites, that I can add to settings so it can find the metadata?

Concerning Calibre’s interface on the left side panel, where it shows the categories you can sort by. Is there a way to create new categories for sorting your books? For example: creating sub-groups that you can drag & drop your books into (organize/sort them better) like: Books, Educational Books, Comic Books, Light Novels, Manga, & etc?

Are there any good plugins, interface changes or other suggestions that anyone knows that I should be aware of?

Any information about the matters above would greatly be appreciated, thanks.