Ok, so I would like to use (or at least try) Skyrim HD, but I do not wan't whatever SKyrim HD contains to overwrite the High-Definition Texture Pack DLC. How can I do this? Can I?

Do I need to make entry's into the base Skyrim.ini file under [Archive] for each .bsa file? I'm not sure, figured I would ask around and see if anyone knew.

Well, if SkyrimHD is loose files, you can't.

If they're BSA'd, simply make the associated ESP modules load before the official HD tex pack's. Content conflict override occurs in the following order: INI-loaded BSAs first (the vanilla BSAs, basically), Module-associated BSAs next (in the same load order as their associated modules), and then loose files last and on top.

First - If a bsa just contains replacer textures (textures with the same name and path as the vanilla game files) the game will use those instead of the games

If a bsa comes with an esp with the same name as the bsa, you dont need to edit your ini, the game will load the texttures from the custom bsa

Now, which textures you get in game depends on the load order of the bsas (by virtue of where the corresponding esp is in your load order), last loaded wins if both bsas are replacing the same textures.

It may be that Skyrim HD only includes some of the textures in the DLC (I dont use either so cant say for certain), so if you load Skyrim HD bsa last out of the two, its textures will end up in game, and what it does not replace from DLC textures .. Those will also be in the game overriding the game originals.

example ..

game original bsa contains
path\texture 1
path\texture 2
path\texture 3

dlc bsa contains
path\texture 2 <-- Overwrites game original and ends up in game
path\texture 3

skyrim hd bsa contains
path\texture 3 <-- Overwrites dlc and ends up in game

so you end up with
original texture 1
dlc texture 2
skyrim hd texture 3

If you changed the load order so that DLC follows Skyrim HD, you would have
original texture 1
dlc texture 2
dlc texture 3 <-- Overwriting Skyrim HD

So it becomes a big job, if you want to get detailled on what you want in game, you could use BSAOpt to extract Skyrim HD bsa to loose files, then remake it without the offending textures, or just install them as loose files (not in a bsa), which override all textures in all bsas.

Loose files always win. But obviously if you have two mods with the same texture and path, only one can be installed because it will overwrite the other.

See also the following two topics ..
http://www.gamesas.com/topic/1354395-update-bsas-and-you/
http://www.gamesas.com/topic/1356991-important-load-order-and-you-2/

Edit: For anyone that doesn't know, a bsa is Bethesda Softworks Archive, its like a zip file containing whatever resource. The bsa is treated by the game as an extra data\ folder (even though it is inside the data folder), and if it finds a Textures folder in the root of the archive, it treats it like a loose Textures folder in data\. But an actual loose Texture folder will have its textures win over any textures with the same name in any bsa.