The right way to go about creating a WordPress site from a static site which has WordPress installs in its subdirectory

Well it depends what is suitable for you, as you said :

I’ve added in two WordPress installs in subdirectories, one being a
blog page and another being an eCommerce site

and now you want to make your static site dynamic with WordPress, you have options, either you can merge all your sites in one WordPress installation OR install a new WordPress for your main site.

i would suggest, you should merge all your sites in one IF they both are on same domain, you can find any suitable theme similar to your design or you can also convert your static site in WordPress theme.

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