I don’t think this is a theme related issue, is it? Wouldn’t you have exactly the same issue if, for example, you were using one of the default WordPress themes?
Let me google that for you → http://lmgtfy.com/?q=wordpress+add+jquery+script+to+page
Please always keep in mind that our theme support is only for issues that are directly related to the theme, we can’t help with generic WordPress issues. If you believe the issue is related to the Traject theme, please switch to a default WordPress theme, such as Twenty Fourteen for example, to see if the issue is still there or if it goes away. If the the issue is still there then the issue is not related to the Traject theme and so we can’t help with that issue.
For all generic WordPress issues there is a dedicated support forum → http://wordpress.org/support/
If after switching themes the issue goes away then the issue might be related to the Traject theme, in which case let us know and we will work from there.