format the clean game should be
Clean game? Any pirated game, and/or Modified game is not clean, and if you are installing pirated games/ Modded games, make sure you're only doing this on emuNAND, pretty much guaranteed a ban if you do it anywhere else, Nintendo will know you don't own it the second you go online, and/or will know if it's been changed majorly or modified. The only "clean games" are ones you get from Nintendo directly.
As for the formats:
NSP = Nintendo Submission Package
XCI = Cart image
Tho do remember, if your game is pirated, and it's too big, depending on how your SD card is formatted, you might need to use an NSP splitter to split the game up into multiple parts,
for example it's kinda like how with .rar files you can split them up into multiple parts, look for tuts on youtube on how to make large games work on the SD card.
Do you mean cheats? or mods?, "hacks" is kinda a weird description for either of those... for either of those look on youtube to get an idea how to use those thing, I know there is a simple mod loader you can get to handle enabling/disabling mods, and if you meant cheats/codes look up EdiZon, that would be a good place to start.
And if you mean like RomHacks, like a fan game or somehting... Install them liek you would any pirated game, or apply any mods if it's a mod or install it as a DLC style "3rd party" update that goes over the original files, Kinda all depends on the creater of the RomHack, and how they packaged up the game, being that could change depending on who made it. Best to look up instalations tuts on the particular RomHack you have interest in.