You can use script-like tags there, but you would really need to build on top of the XF framework and use <xf:js> tags similar the core. This will ensure that your tags are only loaded once and will be dynamically loaded when needed. You can use something like:
<xf:js src="path/to/file.js" />
This path is relative to the js/ directory within XF.
Alternatively, you could potentially just add your tag to the bottom of the PAGE_CONTAINER template, though I'd recommend building on the XF framework as there are situations where this won't necessarily work.