So im gonna download the CS and on the page there are two versions, a v1.2.404 and a patch for it that says that one lets you modify SI and KotN content, and theres a 1.0 version that says it lets you modify Oblivion.

I DO have the GotY edition so I do have the SI patched version of Oblivion, but I don't see myself doing anything to SI or KotN content. Do I still choose the v1.2 or do I go with the v1.0

If you intend on making quests with voice files, you'll want both. IIRC, the 1.2.404 CS is broken in regard to lip files.
Otherwise, just grab 1.2.404.

this causes so much confusion, they really need to update that page to stop these thread popping up every fortnight.

If you use the 1.2 patch in your game and you arent planning on my making vioce files you use the 1.2 version.