My current Witcher 3 patch version is 1.04. I want to upgrade it to 1.06. But will the 1.06 have the updates of 1.05, or do I have to install both in order, individually?
They should all install at once. When you are updating your game to version 1.06, you are not simply installing the 1.06 update files, you are updating the game to be version 1.06. Version 1.06 includes any versions leading up to 1.06.
That is, if you are currently at 1.04, then to get you to version 1.06, it will have to install updates for 1.05 and 1.06. It will do this for you. It will take longer to update from 1.04 to 1.06 than from 1.05 to 1.06 simply because updating from 1.04 to 1.06 also includes the 1.05 updates.