Apple made some changes to Mac Mail in Big Sur (and, presumably, forthcoming versions) that some are finding disorienting.
The old behavior, as it has stood approximately forever, is that the “special folders” of accounts—Inbox, Sent, Drafts, Junk, Trash, and Archive—were collected together and shown at the top left in the column of mail folders and accounts, and could be viewed mixed together, or individually. Any additional folders, such as filed mail, were then shown per-account, each in their own section, below.
The new behavior, which I personally don’t love but it is what it is, is that that the Inbox, Sent, Drafts, Junk, Trash, and Archive folders for each account are now shown within each account below, in addition to any other folders present, whereas they used to be hidden and only shown up top.
However, the old behavior is provided by a new “Favorites” section at top left, and it is here that the Inbox, Sent, Drafts, Junk, Trash, and Archive folders are shown aggregated, as before. But, by default, not all of them are shown—you only get Inbox and Sent. To restore the rest of them, you need to click on the tiny + sign to the right of Favorites, and then enable what you want to see.
Mail then appear much as it did before, except that the Inbox, Sent, Drafts, Junk, Trash, and Archive folders also appear under each account, below the Favorites section. What under “Favorites” can be thought of as shortcuts or aliases to the folders within each account; it doesn’t matter which you use, except that Favorites does allow you to see multiple accounts mixed together.
One nice improvement is that you can designate any other folder for the Favorites section as well by control-clicking on it and choosing “Add To Favorites.” So if you have a couple of filed mail folders you want to be able to quickly get to, you can have them also appear in the upper left.