In my first screenshot below, you will see what the Gmail folders should look like in Thunderbird.

You have to change the default settings in Thunderbird for the account to use these Gmail IMAP folders, otherwise Thunderbird will create ones that are not in the correct location.

Right-click the account in the normal folder view of Thunderbird, and choose Settings.

First up is telling Thunderbird where the Trash folder is. That is set in Server Settings for the account. See my second screenshot below.

Next is the Copies & Folders section, my third screenshot below. Set the location for Sent and Drafts to the corresponding folders Gmail has designated for them. Gmail doesn't have locations for Archives or Templates, so if you want to use them, you should first create the folders in the normal folder view for them as sibling folders to Drafts, Sent Mail, etc., then set the locations here in Copies & Folders.

Lastly, you set the location for the Junk/Spam folder, under Junk Settings, my forth screenshot below.

This is all necessary because Gmail doesn't have it's folders where Thunderbird expects them.

Hey, thanks a lot for the reply. I looked into this before you replied and I think I managed to sort it. I saw from Google's own recommended settings for Thunderbird, that they suggest to UNtick "place a copy in" and to UNtick "enable adaptive junk mail". I think doing both will use the Gmail defaults?

It seemed I couldn't delete the non GMAIL SENT folder in thunderbird, but ensuring both labels were empty in Gmail, I deleted the labels from Gmail and on the next restart of thunderbird, they were gone and it all seems to be working fine now :)

There are ways to "flatten" gmail's default folders system, which can make it look nicer in Thunderbird. However, in other email clients used on the same account, it becomes more ugly, usually with a compound folder name/pathname.

I'd recommend you learn to live with it, unless you expect never to use your gmail account in other clients.

Under the hood, gmail stores all of your email an one big folder named All Mail, and each message is labelled. Accordingly, Archives, Sent, Trash, Junk etc are all stored in All Mail (but with appropriate labels) and I think that's why they discourage some folders in Thunderbird and other email clients. Doing so might put some messages where Gmail cannot easily access (or analyze?) them.

I don't think any of this has any impact on the pre-configured nested folders.

For the record, I use both Thunderbird's Junk Controls and Gmail's spam detection in the same account. In one of my gmail accounts, they regularly miscategorize good messages as Spam, which is most vexatious, whereas Thunderbird's Junk Controls have become very effective for me.

Thanks a lot for the input. I actually have a few account filters set to never send to spam anyway so I'm not so concerned with missing mails. I've also simplified my gmail inbox so I don't have the what is now default categories, I just have the inbox.

I know you can hide labels and choose to hide in imap too but for the initial problem with the sent/trash folder, I wanted to get rid of it completely, which I did by deleting the label and the delete was reflected in thunderbird too, even though I think the folder was initially created in thunderbird so I was happy to see it removed, I didn't think it would work but it did :)