Go to the screen where you pick a certain amount of $ to add to the eShop. There are 4 options, right?
Are they: $10, $20, $50 & $100?
$5, $10, $20 & $50?
Mine are the former, used to be the latter 'till around xmas time. I used the $5 option a lot with $25 prepaid credit cards. I contacted Nintendo's customer support email thing and got a response that said it should be the latter showing up...
The "add needed funds" button is also there for a reason. Click the download button when you have insufficient funds, it'll prompt you to add funds. Click "add needed funds".
That method doesn't work for people that are saving up...
Like, lets say "Bob", or whatever, has $60 in the eShop. He needs to add five to spend so he can still have $60 for FE:A & BA:CT. He won't be able to use the Add Needed Funds thing 'cause there is no $65 thing in the eShop.