How Do I *sigh* I have come to the realization that I need to do a complete re-install

If you have packed and extracted the houses from the original Epscot hood, you should not have to change anything. Just install the sims2pack file, and move the house from the bin into the hood.

Answer regarding placing houses: If the houses are sims2packs - you don't need to do anything. You just install them, like BO says.

However, if you're talking about N005- prefixes, there's a good chance you're talking about the package files. What you do with these is put them in your lot bin folder and then they will turn up in your lot bin to place.

Sub hoods are linked to the main hood - so if you have 6 different main hoods, then you'll have 6 different sub hoods.

The empty houses are S2packs, but the occupied ones were just backed up in their N00# form. I'm not gonna blow up, am I?
Will these houses install as empty? (Which is what I want!)

Occupied lots in that form? Yes, they will probably install empty, because the referenced sims will be missing. But the references will still exist and cause grief in the long term...
You should have packed those too, and then cleaned them up. And by cleaning up, I mean removing all references to sims that don't live in the lot.
The cleaned-up & packed occupied lots could then have been installed properly as well, and you would have had the choice to include or exclude the inhabitants at will.

Since I want them to be empty... is there a way to clean out those references before installing? (Thanks, BO!)

You could temporarily dump the lot in the bin, then move it from the bin to a temporary 'test hood', and then package it the way you should have. Then open the package in Sim2Pack Clean Installer, unselect everything except the lot segment, and then save the package with a new name. Then throw away the old Sims2Pack, and install the new one in your actual playable hood.

That should normally take care of it. But just to make sure, you could also the the Lot Reset object (I'm not sure about its name) from MATY, and use that object from within the lot before you package it.

OK - thanks I'll try it.

Nods. What BO said.

OK - I'm stupid. Where exactly do I put these? How do I get them into the lot bin? I tried in 3 different places and none worked. I tried:
-Doc files - lot catalog (with all the csx - or something files)
-Doc files - Neighborhoods (both, putting them all in with N001; and also putting the N001's with N001's, G001's with G001's, etc)
-Prog files - N'hoods, same as above.

I've probably broke everything... I also made a mistake and had an owned business in my folder (I forgot Morti Goth owned it) It was one of the few lots that actually showed up. ...And I opened it before I remembered it was an owned business. Yikes. I WAS trying to only put in my empty houses - do I need to start over? Out of probably 80 or so empty lots, only 3 appeared - all in P-ville, and all businesses (one owned.)

Another thing I can't find - I'm going to make a custom downtown for Belladonna Cove. I've already set it up in game, and added one of the bin lots as a sort of place marker. Now, where is this neighborhood stored in my program files? I looked all through the Apt Life N'hood and User data/N'hood, and through My Doc/N'hood files - I'm not seeing a new N'hood anywhere??? But, yes, it is there in-game.

AAARgh! I'm drowning! Actually, I'm going to sleep - hopefully, in the morning, my head will be clearer, and ya'll will have provided your insightful wisdom to this thread. THANK YOU!!!

Can you parcel them up and send me a link - and I'll have a look and see exactly what needs to be done, in my game.

The first folder you put it in, should be the folder that worked.