Does connecting to existing domain overwrite the existing site completely?

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I have an existing site and I want to use Shopify to fix up my store. Issue is, my products are HUGELY customizable, so several products are easily going over the 100 variation limit.
I know there are apps that bypass that, but they seem to only effect the Shopify store, not the buy now button I want to use. I’m not sure about connecting my domain to the store, as I have some pages other than the shop (such as one with a lot of making of videos) that I don’t want to lose as it’s not like the Shopify store has options for those.
Is there any way to just have the connection be to the store ( ex: mysite.com/store ) and not have it take over the rest of the site? Or just imbed the specific product listings from the Shopify store rather than the product listing?
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