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My website is mostly blog posts. I have the same header and navigation menu on all pages. The header, apparently, has my site title as paragraph text.
I was just running through bing webmaster tools and it gave me an alert that all my pages are missing h1 tags.
I changed the post template to put the article title as h1, but how do I fix the homepage issue? If I change the header navigation to have h1 as my site title, then I’ll have two h1 tags on all of my posts.

Yes, an H1 tag is a critical part of good SEO.
On a blog post single page, the blog post title needs to be the H1 – the website title should not be h1. There should only be 1 H1 tag per page.
Can you share a link to your site?