https://3ds.hacks.guide/
Use at your own risk. Use whichever version that works.
I personally recommend ntrboot, since it works for all 3DS/2DS and firmware, but you'll have to purchase a NDS flashcart.
Since this guide is usually more updated than videos (it's hard to update a video, besides dropping another link in the description, and that may not happen) I prefer this guide.
Plus every time I hacked a 3DS (whether mine or someone else's), the contents change (yay for progress), so read it up.
You'll be able to (for .cia), but if you download them from sites (and didn't dump them from carts) that is piracy.
Against our rules to discuss where to get them or link them.
A save manager (JKSM or Checkpoint).
FBI (some people use it to install apps, tho to prevent being banned, doing stuff homebrew stuff is typically better).
GodMode9 (while it's an alternative loader, and not an app per se, you can use it to convert your carts to .cia)
Using their official services, you'll need a Bank subscription to send to Bank,
then a HOME subscription to send up to from Bank to HOME.
Via PKHeX. Just create mons legally.
Can't read your mind, can't tell the future.
It'll be tough to know what you really need.
Well, we got some tutorials, read them up, if relevant:
https://projectpokemon.org/tutorials/