If you’d like to use Amazon Gift Cards with comiXology, you can just use them on Amazon.com for Kindle Comics with Kindle & comiXology badging. After purchasing, you can then read them on comixology.com with your Amazon account. If you have a comiXology account, you just need to merge with your Amazon account to have the books sync over for reading.

Here is an example of a book with that badging.

And here is where you can merge, if you had a comiXology account and haven't done so already.