How do I change the Mail settings to view all 3 email accounts and folders?

Give this a try: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE 1: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

NOTE 2: if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode. This makes it act as a wired keyboard as will insure a successful boot into Safe Mode.

Have you tied hovering over the"+" sign to the right of a mailbox which opens a pull down menu and then look down through the menu and select the folders that were missing. Or also see if there is a ^ or > symbol next to the "+" sign which will expand the current mailbox.

Try going into System Settings, Internet Accounts, And insure each of the mail accounts is enabled.

Example:

Could this be the case?

Good news.

Try removing one account from Mail's Accounts settings pane and then add it back. See if that helps.

Thanks for letting us know. Sometimes getting back to basics is the best solution.