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if you want separate accounts, just set it up on her computer. if she wants to use it to load books, it will be obviously easier this way. she can load books other ways, but if she's not good at computers, she might not like them.
it partly depends where she intends to buy/obtain books from....kobo bookstore only, multiple ebook stores, borrow from library, download classic books from places like gutenburg.org??? If she only ever plans to buy from kobo, cause that is convenient, having the desktop app will be handy. if she plans to do other things, it might be less useful.
as GeoffR says, for setup, over wifi is simple. you may still want to put the desktop app on her computer for her convenience afterwards though. no point at all to use your computer for both setups, unless a) she can't manage to buy her own books (seriously lacking any tech skills) b) you want to share an account and all books and use one credit card.
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