Applications :: Three Email Accounts - Getting Organized In Mail

I've only really used Mail in a very basic way - for reading email from three email accounts, one work, two Gmail. I've never attempted to organize things in any way. However, I want to clean things up a bit now. I'm getting a lot of work emails - I'm a journalist - and I want to organise them based on which article they relate to. I presumed the easiest way to do this would be to create a folder (a 'Mailbox' I take it, Mailbox > New Mailbox) and drag the relevant emails to the corresponding folder. However, when I do this the emails no longer appear in my overall Inbox, so when I search the Inbox, they don't appear. I've had a quick look around the Preferences, but can't see a simply option for changing this. Am I going about this the right way organising using Mailboxes? Or is there a better way perhaps?