Some people use a third party program for that. Mailbag assistant has a good reputation.

I used to have a dummy account in TB where I stored my archived messages in different folder, but nowadays I've just got an archive folder  with several subfolders in my only mail account.

I don't know how often you want to access that archive, but another option would be to create a dummy account.
Close TB.
Write the account directory for your dummy account to CD or DVD.
Start TB.
Delete your dummy account (including the message base)
And whenever you want to look into your archive, you just create your dummy account again and point it to the CD.
Unless you're always keeping the CD in the drive, it's a bad idea to keep the archive account, because TB wants to be able to access its active accounts.