I want to have two different themes, one for the general site, and another for a section.
When I did some research on how to go about this, this suggests creating a separate static site:
I am wondering what is the best option? what are the advantages or disadvantages of having a separate site that looks like a part of the same site, versus having a section?
The question is where you want the complexity to be. It’s up to you. Do you want to put the complexity in the theme or the deployment?
By ‘deployment’, do you mean deploying parts of the site separately?
Yes, that’s what I mean.
Yes that might be useful, in that case would I do this by having the separate static sites option?
Yes. Separate sites is the complex deployment option, although I don’t think it’s overly complex.
If I have separate sites, can I still have them under the same domain??
Yes, we have some mini-sites that we deploy as sub-directories on a larger non-Hugo site.
Wouldnt this be regardded as two different sites b Google and Google Analytics?? Im just a bit concerned that this wont be regarded as the same website, and that its just a lazy workaround
We already do this in production and use Google Analytics.
Nothing lazy about it. It’s just static content. It’s not that complicated. Use the same Google Analytics ID, and you’ll be fine.
Could you direct me to information that tells you how to configure either separate sites or subdirectories, as I have need for both for different projects.
Also you mentioned you also use a non-hugo site, could you talk about how you use Hugo with a non-Hugo site? thanks
So the following is achieved with two separate hugo sites:
(sorry I dont mean for you to repeat yourself, I just want to make sure i have understood correctly)
Yes, that’s what I mean. 
I don’t know how to do this.
In Hugo, all you really need to do is manage your baseURL config option. Everything else is just putting the generated site into the right folder on your website.
If this is too much for you, circle back to my original reply and put the complexity into your theme.