Super vague post, Eno.
When people say they are using a texture pack as a base and then applying textures on top, they mean that they are copy/replacing one pack after installing the first. This is useful because there are some packs that replace most textures and some packs that only replace specific textures.
So in my case, I use Visual Pack as my base and then I apply, say, AOF's Hlaalu on top of that. I'm not changing Visual Pack, I'm getting rid of Visual Pack's Hlaalu textures in favor of AOF's through copy/replace.
I hope that's what you were asking about.