The oder code you can add manually into your template / templates / index.tpl in the section. For a script code don't forget to use the "literal" tag like:
Avoid making changes to distributed code. The product has matured to the point where this is rarely necessary. You can use template hooks to do most of what you need (search Google for "cs-cart hooks").
This will probably not put the code into the 'head' section of the page.
No it won't but it probably doesn't matter. Most 3rd party scripts are more dependent on "order of execution" than they are of position in the source. I.e. as long as a script is initialized before it is referenced, it is probably irrelevant whether it's in the head or at the end of the body. You can use the scripts.post.tpl hook to get things into the head if really needed. But all scripts in the body are deferred to the end unless they have the data-no-defer attribute (like for a map, or graphic object). Note that the order of deferred scripts is maintained.