Organising mail in Apple Mail using folders/mailboxes

What is the best way to have a folder system where I can still see the emails in both my inbox and the folder?

Not possible in Mail. They have obviously made some semblance of capability to work with Gmail's goofiness, but if you look at a lot of posts here, it doesn't work very well. Sometimes the files move, sometimes they come back, sometimes they got lost completely.

If you want Gmail's labels, use Gmail from their web portal.

You could use Smart Mailboxes to achieve where you could see messages from multiple locations all in the same folder. Perhaps by using a single Flag to mark messages you want to view in one Folder. Make a Smart Mailbox that shows messages marked with that Flag.

Here's what I do. I create Mailboxes under On My Mac for those senders that I what to save and isolate. I then create rules for each sender moving the email to the appropriate mailbox.

I also have a smart mail box titled Unread which is like this:

That way I have a virtual "inbox" of all incoming email. It if read an email it will be removed from the smart mailbox. If it delete the email from the smart mailbox it will be deleted from the mailbox it was sent to.

I have quite a few mailboxes, about 100 of them, for different senders and topics