The best thing to do is start with a completely blank ET install (just install it to a new location). After extracting pak0.pk3, you will have all the textures that everyone will have, and you do not have to add them to your map PK3 file.
Once you find the need to add a custom texture (or a texture from another custom map), you create a new directory in the etmain/textures directory, with the name of your map. You place the texture in that directory.
You can now use that texture in radiant, and it will show up under the category that is named after your map. This way, you know instantly that it is a custom texture and that you will have to include it in your pk3!
When you now make another map, you will obviously have the custom textures from your first map in the textures directory. However, because they appear in the texture browser under the category of your first map name, you know not to use them (and you shouldn’t!). Should the need arise to use a custom texture that you also used in your first map, I always find it convenient to simply copy the texture to another texture directory (named after your current map now). So you could have a few textures multiple times in your texture directory, but at least you know that all you have to do is add the texture directory of your current map to the pk3 and you will be fine! If you don’t copy the texture over, you will need to remember to add the texture to another directory in your pk3, something that is likely you will forget…
So just start with a fresh install, and put every custom texture in a new directory named after your map. Then all you have to do is put that directory in your pk3 and you should be fine.