Will my glossary look the same as my site?

If you prefer, yes (subject to the limitations of the page structure of the glossaries). 

We will create the layout of the site based on the design manual you provide, and since the whole site structure is designed without a top menu bar by default (this is also good because of the primacy of the mobile view), it can take over the menu structure of your site if you want.

If you have no specific layout obligations, you can also set the basic layout settings for your site (e.g., colour, font) in the admin interface.