IMO the first thing to do is to look for the index.template.php file inside your SMF themes/TemplateName/ folder where TemplateName is the name of your SMF template.
Inside the index.template.php file you will find three functions: template_init, template_main_above and template_main_below. The template_main_above function is used to render the top banners and menus of your smf page. This is the function you will need to modify to include your MODx menu file (e.g. include sitemenu.php).
You are saying getChunk... does that need to be a chunk with my CSS information pasted in? And then the Drop menu or Wayfinder call.
This is optional but yes, the css (if any) for the MODx menu can be added to a chunk. You can also choose to insert the css code directly inside your SMF template.
Do I need to be inserting some of my main template code into this PHP file to get the full layout? Or does that goes in the SMF template with this PHP file called in the exact location where I want the active menu to appear?
The modx menu php file is primarily used for getting the menu from modx. If you would like to add some additional HTML code to your SMF template then you can choose to either insert it inside the sitemenu.php file or inside your SMF template (index.template.php).
Hope this helps.