If you've been using Airmail for some time (or even if you're new to the app), you might have noticed some of the funky folders in the lower left-hand corner which give the app a bit of organizational flair.
Two of these folders - Local Sent and Local Drafts - can cause some initial confusion without some additional tweaking. By default, Airmail uses the Local Sent folder to store emails you've sent bypassing the server's own sent folder. It sounds logical, but it can wreak havoc on your email organization if you're not careful. I've written a previous article outlining how to deal with this issue, if you'd rather save your sent emails to the server, rather than locally.
Overcoming the default behavior with the Local Drafts folder is a bit more challenging. In its current iteration, Airmail will always want to save email drafts locally, but you can modify this behavior to allow it to prompt you with what to do with saved drafts.
Start a draft email and attempt to close the window (⌘ W). You'll be prompted with the following drop-down dialog asking where you'd like to save your draft. Choose Save Online to save it to the drafts folder on the server and have access to it on another machine or your smartphone for finishing later.
Unfortunately, there is no way to save this behavior as a default: you'll have to choose this option each time you want to save a draft to the server. It's because of this I don't draft nearly as many emails as I used to.
If you do opt to save your drafts in the Local Drafts folder, there's a handy option in Preferences (⌘ ,) --> Advanced --> Local Messages drop down labeled Remove Always. It's my understanding this will keep your local directory for drafts tidy, but as with any software still under active development, YMMV.