When you say "preview" do you mean in the Bootstrap studio program window, or in the web browser preview that you open up when you click the Preview button in the upper right? You will never see your custom javascript running inside the BSS program, but you should be able to see it in your web browser preview.
If you are referencing jquery in your custom code, you do have to change the location of the jquery library to make it work in preview, vs the location in a live uploaded website.
On this site, I'm using a popular particle generator to make the "soap bubble" effect... www.formulaautowash.com I'm only doing the bubbles on the home page. I created a new .js file by right-clicking the JavaScript folder in the design panel at the lower right, and pasting into it the code generated by the particle.js program. So this gets loaded on every page of the site by default. I'd rather it didn't, but I can't control that.
On the home page, I have a single custom code element in the tree right after the Body component. This custom code component triggers the particle script to run, and it contains the following code...
<script src="assets/js/jquery.min.js"></script>
<script src="http://cdn.jsdelivr.net/particles.js/2.0.0/particles.min.js"></script>
Without the first line telling the code where to find the jquery library in the preview mode, the effect would not run. The actual jquery library that Bootstrap Studio uploads when you export your files is different, and this is the path. This cannot be changed, and is done automatically by the program...
<script src="/js/jquery-3.4.1.min.js"></script>
I don't know if this helps you at all. Not long ago, I requested that the devs give us an option to add custom HTML before the head, inside the head, inside the body, or after the body. I don't know if they've taken it under advisement or not.