Don't worry, what you thought is right. Just delete the old SMS.elf in your MC and copy over the new one and rename to SMS.elf. You can do that to latest uLaunchELF als, rename it to BOOT.elf and copy over to your MC. Just use uLaunchELF's regular copy/paste commands as these are enough for normal files. MCPaste is used for game-saves which store extra data so it will copied fine to your HDD and vice versa. Use MCPaste only if you copy over (backup) your game-saves on your HDD or USB stick. Good luck.
PS2 30004R, FreeMC 1.8b, Maxtor 160GB Slim HDD, SMS 2.9 R4, uLaunchELF 4.42