For modules with simple/limited amounts of Javascript, spend a bit of time understanding the concept of the Naming Container and the need to pass the ClientID (rather than simply the ID) of controls into your JS methods. For more involved Javascript needs, look into client-side scripting using component, behavior, control extenders, script controls, etc. provided in the MS AJAX framework and MS AJAX Control Toolkit. You'll also find some interesting reading about the DNN ClientAPI and DNN Control development on Jon Henning's website http://www.codeendeavors.com.

Communicating between .ascx and Javascript without using ClientID is possible with this free control : http://code.msdn.microsoft.com/RegClientControls

RegClientControls can make caller from external javascript into your web form control ID without using <%= ... %> again.

It is really helpfull. Try that !

HTH.