Hello,
at the moment you can alter the current behavior by creating a separate set of folders under Local Folders (e.g. [email protected], [email protected] or even two folders email1… and email2 with Inbox and Sent as subfolders) and create rules that will move incoming emails into specified folders based on the account (Tools->Rules). Similarly outgoing mails can be sorted this way. Please note that this behavior is exhibited only on POP3 accounts. IMAP accounts conversely always have separate folder trees.
Also other users on this forum who use IMAP accounts have suggested that they would prefer having their accounts merged into one folder, so both models have their promoters.
Therefore, in the future we probably will add functionality allowing a user to choose whether to create a separate folder tree - I created and idea you can vote for at https://discourse.emclient.com/emclient/topics/separate_folder_trees_for_accounts
Best Regards