Look at Message Filters.

Zenos said

Look at Message Filters.

could you be more specific?

The usual way to automate the filing of messages is to use Message Filters. These are found under Tools|Message Filters in the traditional menus, or under Message Filters if you use the new Application Menu button, [≡].

There is an add-on:

https://addons.mozilla.org/en-US/thunderbird/addon/quickfilters/

which may be attractive if you use filters a lot.

BTW, it's perfectly normal for all incoming messages to land in the Inbox, regardless of their context. Indeed, many Thunderbird users find it hard to work with each email account having its own Inbox, and they are panicked by needing to manage multiple Inboxes, and prefer to herd all incoming into one common Inbox.

So you're in a bit of a minority in wanting incoming unread messages to be filed straight away. (I do the same myself, with circulars and trade magazine postings. They don't NEED to be read and can be safely filed away awaiting some free time.)

Thanks for you help, but I feel like I'm only getting generic answers. I use thunderbird for work, and have a lot of filters automatically filtering my hundreds of emails already. Unfortunately my filters don't catch ALL emails so some must be manually moved to certain folders. So when I manually drag a certain email to Folder A, I would like all following replies (set and received) to that specific email be threaded below said email in Folder A. Right now, if I get another response I have to manually drag that email to Folder A. Once I drop it into Folder A it seems to sync up with the previous emails in the thread that came before it. I just don't understand why thunderbird doesn't do this automatically.

This isn't something that can be done by filters, It should be a setting or something I'd presume. My question is can this be done? Is there an add-on that can achieve this?

No, I don't know of any add-on to manage threads in this way. Thunderbird will indeed assemble related messages into threads, but there's no mechanism, other than filters, to move threads into specific folders.

You might find the "Copy Sent To Folder" add-on useful, but it only deals with the business of placing a copy of a sent message in the same folder as you were in when writing a reply.

Gotcha, thanks for your all your help Zenos!

My ideal function would be that the emails(that aren't filtered) are first sent to my inbox, after they're read and closed or when I hit a button, all the read emails in my inbox would automatically be sorted to where ever the rest of the thread is contained. I'm sort of surprised no one else would want this kind of feature.

Well if anyone happens to have any insight, please let me know!

The conversations add-on finds mails and stacks them in a gmail type view...Instead of a thread is does the whole gmail thing.

The view mail in conversation (Ctrl+Shift+O) native function also will locate appropriate mail and place them in a threaded view, but it does not actually move anything either.