You didn't say what mail app you're using and which OS X version, but lets assume it is Mail and Mavericks ...
I regularly backup /Users/myname/Library/Mail/Vx/Mailboxes to a dedicated 64GB flash drive; you might also want to backup your attachments - /Users/myname/Library/Containers/com.apple.mail/Data/Library/Mail Downloads/
If I need to access a particular email, I either search for keywords/dates, or if I know which folder/subfolder it should be in, just secondary click on it and open "Show Contents" in a new tab (depending on some settings in Mavericks, double-clicking might not work for some system folders, hence 'open in a new tab').
Any message from such a backup can be merged, moved or copied into an active Mail folder structure on another system, which is very convenient, just double-click on email file and select desired action from the top menu.
Or were you, perhaps, saying you just wanted to organize your inbox into folders and set up rules to guide certain emails there?
If my interpretation of your post is correct, you have a couple of options: new mailboxes, or new smart mailboxes.
An example of a typical new mailbox I'll call "spouse emails." I create this mailbox, then set up a rule that all emails from (spouse's email or emails) get moved into the "spouse email" folder. Once the rule is set, the system will offer to search through the current inbox and move those emails as appropriate, and of course future emails as well.
An example of a smart mailbox would be (for example) "all emails from December." A smart mailbox is used when you don't want to actually move messages around, just have a "mailbox" that shows the result of a search on certain criteria. No "rules" need to be set: when you create a Smart Mailbox, you set the conditions and any email that meets those conditions will appear there (but hasn't actually been moved from wherever its stored).