Hi,
I think any related javascript should live beneath the mojoportal site and the third party control should have a configuration option so you can specify the path to the scripts in Web.config. I would review their documentation. Not knowing anything about this control myself I have no idea whether they did make it configurable as they should.
Another thing I would recommend is don't try to add the third party control directly to a page. Instead create your own user control and then add the third party control inside it declaratively with a tag. In other words, host their control inside your own user control.
Hope it helps,
Joe