For three days now I've been trying to put high resolution testures and models into tenebrae. While map textures are no problem, I've been having no luck replacing the ammobox and medkit models and textures. I have tons of the actual art, but where does it go in Tenebrae? I know the map testures belong in ID1\override, but what about models and their textures? Any help would be greatly appreciated.

Dunno about Tenebrae engine myself, you could try the http://www.quakeone.com/ forums.

I think it has a similar naming convention to darkplaces.

In Darkplaces "mdl" models go in "progs/" and textures go in "textures/"
For 24-bit texture replacements for .mdl files, the texture needs to be renamed.
eg for the armour model called armor.mdl rename its textures
eg "armor_0.tga" becomes "armor.mdl_0.tga"
eg "armor_1.tga" becomes "armor.mdl_1.tga"
eg "armor_2.tga" becomes "armor.mdl_1.tga"

In Darkplaces "md3" models go in "progs/" and textures go in "textures/"
rename the .md3 extension to .mdl
eg "armor.mdl" becomes "armor.md3"
but the texture names rename the same eg "armor_0.tga, armor_1.tga, armor_2.tga"

Bakers done a pk3 if you wanna see a example http://www.quakeone.com/forums/showthread.php?t=1343

Renamed you say? Hm.

But where do the progs, etc... folders go? the ID1 folder or the tenebrae folder?

If you use an experimental techdemo like Tenebrae then read the documentation. For example: http://tenebrae.sourceforge.net/index.php?page=technical/textures.htm