For your example, that depends on if you have the ROM or CIA of Fire Emblem (or even the real card). If you have Fire Emblem as a ROM, you put it on a MicroSD card and place it in the red card. Then, with the device in normal Gateway mode, you would tap select, pick your ROM, then hit A, then play the game as if it was a normal card. If you have it as a CIA, you place it on the internal SD card and use DevMenu/BigBlueBox to install it, exit, and then there will be a new package for you to open. At which point it functions just like any other e-shop game purchase. If you want to use the real card, boot into Legacy mode. You could use DevMenu/BigBlueBox to install CIAs of any DLC, updates, etc. you may have downloaded (needs to be placed in the root of the internal SD card). If the current firmware is supported in EmuNAND (which the recent 2.7 update added support for again), you could also get any of the downloadable content from the e-shop.
As for that "EmuNAND jazz" it's basically a virtual copy of your system's firmware. It's stored on a separate partition on the internal SD card. It's called EmuNAND because NAND is the form of flash memory the 3DS uses to store its firmware and settings. There's really not much to it. You set it, and forget it. Once you've had the Gateway software create it, it starts automatically when you go into Gateway mode. It starts out being an exact duplicate of your 4.5 firmware, but you see "GW" in front of the firmware number. You can update it as if it was real firmware (but without losing your exploit). One thing to remember, if you exit the settings menu from EmuNAND, it kicks you back out to your real firmware (this can be inconvenient if you weren't wanting to exit, but it has its uses too). My personal recommendation is to set a theme once you have EmuNAND running 9.x (I like the black one, personally). That way you can tell at a glance whether you're on system firmware or EmuNAND. So, this allows you to run the latest firmware (more or less) while staying on 4.5 for the exploit. You can think of it as having CFW, but the full firmware is actually present. An EmuNAND is a 100% copy, you can even system transfer it to real firmware, but the transferred system would not have any exploits). The Gateway software simply chooses which parts to run, and which parts to ignore. You can therefore access the e-shop and play games with a newer FW requirement. Unlike the PS3, the 3DS doesn't have being on the latest FW as a requirement for online play (only the latest update). So, if you grabbed the latest Pokemon X/Y update from the e-shop before 9.3 hit, you could still have been playing it online on your 9.2 EmuNAND while you were waiting for 2.7 to come out. If not, you could still have installed the update from a CIA.
One thing to be aware of that many people seem to overlook is the existence of a tool called EmuNANDTool. With this, you can backup the EmuNAND partition, and use said backups to revert to previous firmwares whenever you want. Why people continue to update without doing this is a bit of a mystery. Make a backup before every update. Then you won't be one of these noobs that's always going, "omg, I just updated my EmuNAND and got a black screen, help" LOL.
Not that that a messed up EmuNAND is a catastrophe (half of its purpose is to serve as an expendable copy, so that you're not screwed if you brick it). You can always format EmuNAND, taking it back to 4.5. As long as your real firmware is using the same profile (though there's more drawbacks than benefits to that), you won't even lose your purchased downloads (not that lost apps are anything to sweat over, there are CIAs for just about everything, including Netflix and Youtube). Though if you're using separate profiles to keep your EmuNAND icons from showing up in SysNAND (to do this, remove the SD card and format system memory while in normal firmware, note that this will destroy all personal information and settings, and you'll lose any non-built-in apps you had in 4.5, you're basically wiping it clean and starting over as a new user, but it's not like anyone uses real firmware mode for much anyway, you go online, it's going to ask you to update after all), that means your EmuNAND profile is unique now, and formatting will kill it. So, how do you keep your original profile after doing this? Easy. Just use EmuNANDTool to restore your original NAND dump to your EmuNAND whenever you need to reset it, instead of formatting (the Gateway software has an option to create a NAND dump as a safety precaution, creating one and backing it up to your PC is a heavily recommended first step, one that is shown in the video that demonstrates how to set it up at that, so, if you followed the instructions, you're in good shape). You can use a ROM to update EmuNAND if the latest FW is not currently supported (as of 2.7, it is). Smash Bros. will put you on 8.1, the newest any current game requires (just hold up on the d-pad when pressing DS Profile to enable ROM updating). You just might not be able to use all of your purchases until you can get back to 9 (especially themes). So you see, even if you're somewhat careless, it's fairly forgiving.
