I've been dumping through WindHex. Would it be better to use Cartographer?
If you find yourself having issues with Cartographer, I recommend using Romjuice.
Cartographer is handier, once you get it working. But it is far less newbie-friendly than Romjuice. Cartographer, however, has support for dumping Atlas-compatible scripts, so it makes inserting with Atlas that much easier.
(Atlas itself is also not very newbie-friendly, so I'd ask around here if you have trouble using it).