Where to include common HTML <script> tag?

We are attempting to integrate a JavaScript script tag into Akaunting but are running into an issue. We added the script tag to index.php but when we try to log in we are no longer directed to the application. If we refresh the page we land on the Dashboard and the included script functions as expected. We tried just included the script tag without any additional code and observed the same behavior so we're fairly certain it has nothing to do with the JavaScript we're including.

So, the question is: 1) is index.php the right place to include this? and 2) If not, how would you suggest we do this (assuming it's supported at all)?

Thanks in advance for any help.

Regards,
Scott