By default QuickMail opens to All Mail. You can tell it to open anywhere you like instead — one account’s Inbox, a project folder, or All Inboxes.
The quickest way is from the folder tree itself:
QuickMail confirms the change, and opens there every time it starts from then on.
You can also do it from File → Settings → Startup, where the Opens in field shows your current choice. Select Choose… to pick a different folder from the folder tree, or Clear to go back to All Mail. Clear Startup Folder in the folder context menu does the same thing.
If the folder later disappears — you delete it, rename it, or remove the account — QuickMail opens in All Mail and tells you why. Nothing is lost and nothing needs repairing.
Also under File → Settings → Startup, Startup Sync controls how much mail QuickMail checks while it is starting. This matters most if you have several accounts and a lot of folders.
New mail still arrives in your inboxes straight away whichever you choose, so notifications are unaffected. Other folders are caught up by the background check — the Check for new mail every setting on the General tab. If you have set that to Off, other folders are only checked when you open them.