I'm not sure to understand your question. Do you want to simply include your edge animation in dynamic php pages with "php include" or is that something else ?
If I publish an Edge Animate in a folder of my website, for example "/edgeanimate_assets/myedge_animate/", I need to change manually the path in the js files ("myedge_animate_edge.js" and "myedge_animate_edgePreload.js"), otherwise the page in the root (example, /index.php) with edge animate not load the animation.
Yes I know, If you want your edge files to be published in an other folder than the one by default, you have to do it manually, there is not other options in the export settings right now. I do it like this too for the moment.
What you can do if you don't want to rename and change your files after every modification, is to work with a "temporary folder".
So you could for example modify your file as much as you need and then, when you think it's ok, you just replace the edge files that have changed.