Since this is an injected title you have to provide your own iso.
But the application can help you for this particular title since the base game is available on the eShop.
Try saying yes when it asks you to use the game from eShop and you should be good to go.
Make sure the application is not blocked by either your antivirus and/or firewall.
Unfortunately you need to use an SD card that is big enough to fit the entire game.
Thanks
Sorry if I miss a question but this is quite a long post xD
1-Input the 3ds title key site url and make sure the console is enabled in the Filters tab
2-Use the "Copy to SD" button and then install the respective .CIA files with FBI (IMPORTANT NOTICE : Newer 3ds titles have an extra layer of encryption and require a 'seed' to be installed alongside the .cia. This has to be done when installing so USB Helper cannot do it automatically. Most CIA installers have an option to install the seed though).
3-Yeah they do get packed as cia when using the "Copy to sd" button. And they contain a ticket but it is fakesigned.
4-Perhaps it is possible with a custom homebrew for the 3DS but I'm afraid that's outside of the scope of USB Helper so I cannot be more precise here, sorry.
And regarding the DLC problems too, I have in fact little knowledge about the 3DS (the application was for WiiU only first after all ^^') but someone might be able to help you.
5-These check boxes only matter for Wii U titles.
Legit means the ticket was ripped from a Disc and is therefore universal (meaning it can be installed on any system without needing a CFW).
CFW means the ticket was generated by the application. It contains the true title key but is not signed, so a CFW is required (all 3DS titles fall into this category on USB Helper).
Preview refers to some titles which were released before the actual game as a "preview" of the final game (for instance Splatoon Global Testfire)