Mailbox is designed to work with Gmail in straightforward ways, but there are couple of things you can do to make sure your experience is as good as possible:
When a message comes back into your inbox from Later, Mailbox puts a star on it. Gmail lets you show starred items at the very top of your inbox. You can select this option using the drop-down arrow next to Inbox:
If you want to browse your Archive easily, you can make sure Gmail shows the "All Mail" label in your sidebar by clicking "show" in Labels
Mailbox works best when your inbox contains only the messages you need to deal with now. If you've got a lot of email in your inbox that you don't need, use the "help me get to zero" button at the bottom of your inbox in the Mailbox app to clear out the messages you don't need.
All folders created in Mailbox will be located under the [Mailbox] label on the left panel of your Gmail inbox.