Language vs Keyboard Layout
First let's describe the simpler of the two. The keyboard layout is a system-wide state that affects what characters (eg: letters) will be inserted when you press certain keys on your keyboard. That's all the keyboard layout does; it says nothing about the language of the inserted characters. For example, your keyboard can insert a Latin lowercase "e", but that doesn't say whether you mean to type in English, German, French, etc.
Meanwhile language is an attribute of text, like font or color. One can have different parts of a single document marked in multiple languages. It's something permanent that's saved along with the text of your document.
Why is This Important?
If you merely change the keyboard layout, Nisus Writer won't know that you intend to type (or are typing) words in a certain language. If Nisus Writer doesn't know the language, then it can't automatically change language sensitive features like the spelling dictionary, secondary fonts, etc.
How do I Change the Language?
If you are accustomed to working in other applications, it might be second nature to use the little "flag" menu in the very top-right part of the menu bar:
In general, don't use that icon on the menu bar; it just controls the keyboard layout and Nisus Writer won't know the language of your text.
Instead you should change the language applied to your text or styles (eg: using the menu "Format > Language"). If you've correctly configured your Nisus Writer language preferences, changing the language will automatically synchronize language sensitive options like the keyboard layout, spelling dictionary, etc.
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