It took a lot of doing, but I think I got it right. A church and school website that is one but also two. Actually, it's more like three (in one), and it's much more complicated to perform than you might imagine, which is why most church and schools don't have anything like it. Take a look at Calvary Lutheran Church in Murrysville, PA.
Website design is always going to be a comprimise of sorts, especially now with designs that have to look decent and function well in both desktop and mobile. On top of that, when you want two websites to fit under the same domain, combined in some ways but separated in others, you have more negotiating to do. But sometimes, it all works out about as well as you can imagine, and that's Calvary's website by Luthernet.
The main landing page is much more than just that, since you can navigate to anywhere on either the church or school side from there. Because of the complexity of the menus when you do this, it's unheard of from most web designers to add another menu (basically) that only functions on this single page. The menu also has an embedded video, which is just super-cool.
The two other websites are basically /church and /school from the home page, but they are all part of the same domain, using the same users (with permissions based on roles). Each of these sub-sites have their own home page (church and school), and those are also top-notch home pages in their own rights, though maybe not as stunning as the main home page. Technically, I could have done this, too, but it would have required another $1000 or so in time, so we made the decision to make this method work. Keep in mind that the website as a whole came in at under $2000, so even at $3000, it would have been a bargain compared to anything similar from a design boutique. In fact, please feel free to share the link with your local design firm in order to get a quote on something similar.
Each website has its own menu, separate articles, calendars, and modules. All of this can be edited from the frontend. Photo galleries can also be added on the frontend. As well as sermons. There's even an online enrollment form for the school.
There are technically two problems that make this website less-than-perfect. One is that it ended up being a lot of categories to update, and some of them have been ignored while others have been amazing. The other problem that I cannot explain is that the church's Facebook pages, which may be partially private, won't show up using the embedding components I use. Other Facebook pages work fine, but not Calvary's, so we just link out instead. Besides that, this is about as good as any school/church website gets.