Mail mailboxes

My mail program has been getting a bit of a mess recently, i had 4 different email addresses linked to it
-yahoo,
-gmail,
- the one that comes when setting up iCloud,
- and my universities email.

Its become a bit unmanageable due to old rules that were setup, and different mailbox folders making viewing new emails a nightmare.
I attempted to start all over again by resetting it, this involved deleting some folders after reading some thread on how to reset mail to factory settings.
So far i have set up the Yahoo and Gmail accounts again, but i have a problem.

I would like to click on gmail at the top of the list to see my googlemail emails, but for some odd reason only some emails are there, the bulk of them are in the lower down one "all mail (gmail)"

why is there two gmail inbox buttons, how can i remove one so all my googlemail emails are visible from the top gmail tab.

The simple answer to your question is; when you reset Mail and I assume you have a IMAP Google Mail account only new mail will appear in your inbox. All old mail will be archived at the Google server into "All Mail". You should see All Mail under Archived. You cannot change this but it is easily accessed by selecting Archive.