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I am able to generate a schema model ...
Using what tool or product?
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... I cannot integrate it with website ...
Which web site? Yours? A commercial one?
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... they seem rather independent of each other ...
Indeed they are.
A Database can exist without a Web Site.
A Web Site can exist without a Database.
There is no Magic to "smoosh" the two together.
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... it shows the entities I don’t know if it keeps them up to date or not syncing ...
Again, depends entirely on the tool that you are using.
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... I can get that not the relationships and not what is stored by MySql
Unclear.
Step back, take a breath and tell us what you're trying to achieve (your "end game"). There may well be a simpler and better way of achieving it.
Regards, Phill W.