There is no difference. You code in the same elements. Unless you don't know PHP, in which case you are screwed.

Perhaps if you could offer more information about your php pages, maybe some pseudo code or something, you could get more informative answers.

Maybe a suggestion... look at the page source code for an optimized wordpress page and a non optimized version of the same page and find the differences in the html code. And you could also look at the source of the plugins making the changes to see how they're doing it.

Good luck!

That's the least helpful way to describe your site. Every WordPress site runs on PHP so even that doesn't work as a distinction.

You do realize that all the on-page SEO is in the HTML that your code generates, right? There's not much difference between the SEO on any generic web programming language unless the platform itself helps you in some way. But that stuff is probably on CMS or framework level.

Why didn't you go with Wordpress? In a normal website you should code everything yourself.. It's not harder, but how will you add new content? You have your own CMS? In the matter of SEO, you just have to build backlinks... For the On-Page SEO, be sure to check your html files and add the title, meta tags and of course when you are adding the information in your website, optimize it!