My apologies. I also looked over that guide and it has not been updated to reflect the latest GW releases.
the tool is very simple to use. I suggest a second SD card to contain the emunand you use for eshop access. Format an emunand from the gateway menu. Once you have booted that emunand in gateway mode download desired content from eshop. Make a backup of the emumand on PC then mount the Sd card with your playing emumnand and use to tool to inject the backup into the playing emunand. Then copy the folder structure over. Insert Sd in 3ds and boot.
Sounds like your nands are linked. If that is not the case you can try organizing with folders. Sorry that's all I have for you.
"N3DS" is how we refer to the "New 3DS" so be careful around here. You are a buying a "new to you" 3DS or what we are calling an Old 3DS.
1. It will come below 9.2 most likely 8.x or 7.x. Just depends where you get it. It is possible in rare occasions to get a 4.x from a retail store.
2. Not sure what it will want to do out of the box, but it cannot connect to the Internet unless you set up a connection so don't untilmyou are ready. No retail cart has 9.x on it so the highest FW you can update to with cart is 8.x Smash bros has it. 3ds.essh.co lists carts and included firmware. You can also borrow or rent one. 9.5 is what Nintendo will give you if you update online and then you are screwed.
3. You need one mSD gateway and either a mSD and adapter or a SD for the 3DS. At least 4GB for internal SD. An additional SD is helpful when you start switchin emunands around. I personally have Samsung or Sandisk 64GB mSD and two 32GB SD. The gateway will not come with a reader, get an $8 usb from Walmart.
Read, read, read and backup, backup, backup and you will do fine.