Ib4 a9lh link spam with no explanation.
What set up you want and what CFW you want depends on your needs.
The most popular CFW nowadays is Luma3DS as it has regular updates and works on every system. It has all the things one could need (gba Ds patches, emu/sys in front of fw) and works good. Oh yeah, Aurora Wright made a Luma3DS updater cia that you can install to just download the right files immediately from your 3ds if there's an update
which is a nice feature of course!
Besides Luma3DS (previously AuReiNand by the way) you have Cakes, Rxtools (the new version, again), ReiNand, CosmosFW, Gateway and SaltFW. A lot of choice. You'd have to check out for yourself which one you want. Personally I have Luma3DS too
There are two (well three with gateway) set ups you can have. You have either menuhax + CFW, maybe a boot manager, but you'll autoboot into your Emunand with menuhax.
Besides that you can have A9LH: It's called arm9loaderhax. It grants access to the system before the actual boot up of the system because of kernel9 access (not really interesting for normal users anyway). It's basically an exploit that gives you 100% boot rate, the ability to recover from a brick without a hard mod, Sysnand CFW so no more Emunand which saves you the effort to install GBA games twice ect. It does take quite a while to set up but you can find
Plialects guide here if you want to have a look. I have a9lh on my O3DS and it's working perfect. I have menuhax on my n3ds and that's working too (although my boot rate kinda sucks). You'll have to look up what you'd want to have. If you have a day to spare I'd say go with A9LH as it is the best option right now but if you don't, menuhax will suffice as well.