Yeah this is basically how it works:
If you SELECT the brush with the Select tool first, THEN use the Texture tool (SHIFT+A shortcut), it will texture the entire brush.
Instead, deselect everything, THEN open the Texture tool, then start texturing.
And a quick way to use the T tool, instead of selecting a face and clicking apply, simply select the texture you want, then right click on the face you want to texture.
So remember, left click SELECTs, right click TEXTURES. Also, if you want to texture something with a texture you already used, in the T tool you can SELECT (remember that left click) the brushface with that desired texture to select that texture, then right click a different face to texture it.
Sorry if that is confusing, I promise it makes sense lol.