It's not called "Luma3DS.bin" in the archive. It's name is "arm9loaderhax.bin" initially. You have to copy it to the patcher folder and rename it to "Luma3DS.bin" or whatever you want to call it. Then you have to drag it to the executable and type the "[path]/[name]" you want to use on your card (assuming you're using Windows of course, and drag and drop to an executable doesn't work in TC, so, you'll need to type "." and hit enter to open ugly Windows Explorer). Then you just copy it over, and edit your boot manager's configuration file to point to it (if it uses one). Now, if you want to switch to booting Luma straight, and using it's chain loader, you just overwrite your existing "arm9loaderhax.bin" with the one Luma comes with.
Luma neither comes with nor needs payload files. That's just if you want to use it's boot manager. If you're using another boot manager, I would leave it empty. Having two chain loaders active could produce undesirable results. I suppose it's possible to deliberately not use certain keys in one, so you can map them in another, but that could get confusing fast.
Basically, "payloads" is where you would put your Decrypt9.bin (renamed to something like up_D9.bin), Godmode9.bin (renamed to something like down_G9.bin), Emunand9 (renamed to something like left_E9.bin), maybe have a copy of CBM9 for lesser used apps if you're running short on hotkeys (renamed to something like right_CBM9.bin). Of course, the examples are for those who like their tools on the d-pad. And again, only set this up if you're interested in switching to Luma's boot manager. The only manager it might coexist with peacefully is CBM9, because it doesn't use hotkeys by default. Though I don't guarantee you'll have time to hit a hotkey after making your selection. I've never tried it. I suggest making CBM9 your "everything else" page.
As a side note, for those interested, "a9lh.cfg" IS in plain text within the CBM9 "arm9loaderhax.bin" file, so, pseudo multi-page, or even pseudo sub-menus, using multiple copies, is possible. Just tried making pseudo "Apps" and "CFWs" sub-menus, complete with "Back To Main" options. Took 3 .cfg files and 3 copies of CBM9, but it works. Someone convert Retroarch to A9LH. I've got plenty of space for it now
There are advantages to either. If you keep your exiting one, you can hotkey over "B" if you're not using multiple EmuNANDs for example. However, if you're using Luma, you can hotkey "A" and use it with "L+A", so you don't mess up the option to boot default NAND (sometimes you don't want to return to the same NAND when exiting System Settings after all, so you wouldn't want to hotkey "A" while using BootCTR9).