Assuming you are brining them into the same HubSpot account you could push them into seperate Pipelines (ie deal stages, revenue etc), you could assign them to different owners / teams so only specific people can see them or create a property field which indicates which store they can through (good for reporting).
It really depends how you want them to be seperated? Let me know and I can post more details on the solution.
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Ok here is the response I am getting from the app company "Makewebbetter"
Question : Hello, I am using your integration with Hubspot to connect a woocommerce site. I have a second woocommerce site and I am wondering if it is possible to connect it to HUbspot as well maintaining a second installation within Hubspot. 09:37 Hi Brian Kavya Singh Can you please tell me that if you are using free version of our plugin or paid one? Kavya Singh The free version So, you can install it on your other woocommerce site Kavya Singh Ok currently within Hubspot when I go to add another store the connect button is greyed out. Are you saying once the plugin is installed on the second store that the button will be available? A second question is will the contacts from the second site simply be mixed in with the current contacts? If you want to connect your second woocommerce store with single hubspot account, our team will do it for you, we will charge you $40 for that Kavya Singh And answer to your second question, yes your contacts will be mixed Kavya Singh Ok so the only way to have separate contact lists is with a second instance of a Hubspot account. As I understand it the problem with mixing contacts is that of having duplicate accounts. I think if you have the same name and email address it will simply overwrite the current account. That would not be correct since they are truly separate accounts in separate systems. Do I understand that correctly? Hello Brain but there is no way to filter out the contact Vipin
I just looked at the process and it looks like the app only allows the integration of one woocommerce installation. It says the app is installed (which it is) but does not give me a way to integrate a second account.
I am now making an inquiry to the Makewebbetter people as well.