Moving all content that is just pure text information into WordPress is step one.
You must choose if you want to create pages or posts for this content.
As a basic rule (for me), the pages generates the navigation structure for my site, and posts are articles. So one page may list several articles.
Then you might have PHP files that generate content by them selves. E.g. retrieveing data from custom DB.
For these pages, you create custom templates. The easiest way is to add the following at the very top of your PHP pages that needs to be kept as theu are:
/*
Template Name: You custom template name
*/
Then of course add the header, left section, footer etc.
Inside WP just create a page and select the corresponding template.
In this way, you can easy update “static” content by editing pages / posts, and for the custom tempaltes I guess the data needs to be altered in DB or whereever you get the info.
It’s the same process for single and multisite.