Login to sub concrete5 websites from a main website

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I been trying to get this to work.

- I have domain.com (just an html website with php)
- Then I have two concrete5 websites (domain.com/web1 and domain.com/web2)

I have a login screen on domain.com which looks to see if the user is a user on web1 and web2 (if they are a user and validate password - Already got working) then I should set the cookies/sessions.

Question: How do I set the cookies/sessions. This should work at least for one of them because they are sub domains. NOTE: I do not want the same salt for security reasons and other websites I have. I set the cookie but I believe concrete5 does alot more, because it does not work.

Thanks,