You said you downloaded 2 files? What are they? Did you download from both DevHost and Mirror 1? Those should be the same file, and you only need one. Also, flashing MOAR won't get rid of the OTA prompt, as your phone will still report it's on MD4. If all you really want to do is get rid of the nag, flash this file in recovery:
Dev-Host - MOAR_nag_remove.zip - The Ultimate Free File Hosting / File Sharing Service
If you really want to run on MOAR, do the following: This assumes you're currently on the MD4 ROM. If not, let me know.
Boot into recovery
Wipe cache, wipe dalvik cache (mandatory)
Factory reset (optional - see below*)
Flash (install) the ROM file in recovery
-- This will start the Aroma installer, which will give you a lot of options. For the first time, I would suggest choosing "install MOAR as is." Once you're sure everything is working OK, you can go back and reflash the ROM, and choose "Run Morphology ONLY" to choose certain customizations. You don't need to clear cache or Dalvik to run morphology ONLY."
When the install is complete, reboot the phone from recovery.
The first time it boots up, it will take quite a while, and you'll get messages about Android updating. That's normal.
*The first time you install a new ROM, it's generally a good idea to factory reset, to make sure there aren't any files from the old ROM hanging around. Since MOAR is an MD4 Touchwiz-based ROM, it may install OK without a factory reset. But if you don't reset, and start running into glitches, you should probably just start over and factor reset this time. As I'm sure you know, a factory reset will wipe all your application data and settings, so you might want to install Titanium backup and back everything up first.
That's it.Oh, you'll still need to run the MOAR nag remove zip file I linked to above.