What the Options Mean
The wording of these options might seem a little confusing. It merely asks if you want to start the download at that precise moment (Now) or the next time you put the Nintendo 3DS in Sleep Mode (Later). One might be more handy or even necessary, depending on what you’re doing with the device at the moment.
The Download Later option is convenient. For one thing, downloading games in sleep mode is easier on the Nintendo 3DS battery. For another, you can queue several games to download. Then, you can close your 3DS and make a sandwich.
When you want to check the status of your queued downloads, all you need to do is open your 3DS.