OK, I’ll give it a new try after reading your other thread.
Make one site with your first layout with all your needed folders and files (layout, content, config.toml, …). This will generate a public folder. (call this site1 for here)
Now switch to another folder, create a new site will all folders and files - this will give you another public folder. (and this site2)
Now set in your config.toml for site1:
baseURL = "yourdomain.tld"
and in your config.toml for site2:
baseURL = "yourdomain.tld/site2"
Then upload the site1-public dir to your webspace. Create a new folder inside it called site2 (or whatever you have chosen in your config.toml for site2) and upload the site2 public dir into this subfolder.
But doing it this way it might get hard to create links dynamically between your two sites. I think it’s not possible to create two different sites by just calling hugo one time - for deployment in this version you might create a script for calling hugo on both (site1 and site2), merging your public dirs in the correct way and upload the files. You have to decide, which option you will take - I can’t see a recommendation in his words…