Hi Barb
Reading your "Header", I was all ready to offer some advice on how to keep the keyboard keys clean, how to clean them if dirty and similar "housekeeping" chores to maintain a neat and tidy Mac.
Ah well... on to your actual problems
I have never seen any purpose in keeping "1000s" of emails in any one Mailbox let alone the Inbox.
Assuming your email accounts are of the IMAP type, you can pre-determine whether you want to keep your emails "On My Mac" or on the Website account.
For example, if you have an iCloud.com account, you can create Mailboxes "On My Mac" or on "iCloud".
Keeping them "On My Mac" means they stay there and are not synced to other devices. Handy if the great majority of your email work is handled by one Device, say your MacBook or iMac.
If, on the other hand, you regularly check and deal with emails on several Devices, then you would want to sync changes across all Devices - so you would choose to create and keep all your Mailboxes on "iCloud" in the example mentioned.
At the very least, I should have thought that, in addition to your Inbox, you would want "Sent", "Junk", "Trash" Mailboxes.
Mailboxes that reflect your lifestyle - e.g. - "Personal" (with subfolders for Family, Friends etc); "Work" (again with sub-folders relating to companies or individuals); "Online Shopping" (subfolders relating to the common sites you use e.g. Amazon etc); "Internet Articles" (this is for tech stuff and advice relating to your Mac and iOS devices - Mac-Forums, for example).
That is just the beginning. It's all very much a personal choice; but my personal belief is that the Inbox should be as near to empty as possible. You deal with incoming mail here and either dispose of it or allocate it to an appropriate Mailbox.
You can always use the Search function if you can't recall where you place a given email - and the search can be "To", "From" or "All".
A few thoughts, personal of course.
Ian