Righto, here's the skinny on it:
The Main Installer is just for playing the mod with any standard installation of FF7 (Steam, old 1998 PC, etc). It already includes the new field models by default, so no worries about using that separate patch for them. That was more for making those field models available to people if they wanted to use them but not the NT Mod; it's not a proper hotfix patch, strictly speaking (I'll revise the wording of it). The Main Installer is quite straightforward to use; just run it and direct it to the folder called 'data' in your FF7 folder.
The hotfix patches are specifically for fixing issues that arise with the Main Installer's files after it's release, the idea being that rather than having people download the entire main installer again to fix one file it would be better to have a series of smaller patches that fix what needs fixing. The Scene Hotfix patch, for instance, is only 700KB. These are used in exactly the same way as the Main Installer; just point to the data folder of FF7 and it should take care of the rest. The only Hotfix patch required at present is the Scene Hotfix; the other files are all up to date in the Main Installer.
Old hotfix patches, like the Flevel Hotfix, are for people who had the NT Mod installed before the Main Installer was updated. That's why they have the same date as the Main Installer (I'll restructure the lay-out to avoid confusion).
Finally, the IRO File is completely separate from the Main Installer and the hotfix patches. This is specifically for use with a mod-loader program called 7th Heaven (usually called 7H for short). It's a very versatile program that's great for loading different mods together and avoiding clashes between them. It also lets modders use and swap in different assets and affords greater freedom in what we can do with the game. It requires that users convert their copy of FF7 Steam though, which results in the loss of Steam saves and achievements. If you're interested in using different mods together though then it's worth checking out.
So to sum up:
-) Main Installer first
-) Hotfix patches after it (Scene Hotfix only at the moment)
-) Use the IRO only if you're playing FF7 through the 7H Mod-Loader
Any questions, or bug reports, just let me know.