All you should really need to do is make sure every sales page on your site has at least one copy of the E-junkie Cart Script code pasted in, and update the http:// to https:// in any older copies of that code that you'd pasted in prior to 2015 -- e.g., this is what our current Cart Script code should look like in your site:
<script type="text/javascript">function EJEJC_lc(th) { return false; };</script>
<script src="https://www.e-junkie.com/ecom/box.js" type="text/javascript"></script>
This script is what manages the overlay-style cart display within your own sales pages. Whenever the overlay cart cannot work for any reason, any Cart buttons in that page should usually still work in "fallback mode" by opening a new browser window/tab to show the cart. However, due to the way browsers handle cookies, items added to an overlay cart won't appear in the fallback cart and vice-versa, so that explains the "multiple carts" you're seeing.
When you updated your site to load securely with HTTPS, most browsers will block loading any non-secure scripts in a secure page, so older Cart Script code you'd pasted in with a non-secure http:// URL was getting blocked. To accommodate this as HTTPS became more prevalent, the E-junkie Seller Admin/Dashboard has issued all-https:// codes since 2015.
