These options are worded a little confusingly, but you’re simply being asked 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”).
The “Download Later” option is very handy. For one thing, downloading games in sleep mode is a little easier on your Nintendo 3DS’s battery. For another, you can queue up several games to download, then you can close your 3DS and make a sandwich.
Whenever you want to check on the status of your queued downloads, simply open your 3DS.