You will want to call the javascript function Page_ClientValidate() to initiate the ASP.NET validation wired to your page controls. Once this is called, the Page_IsValid boolean value will be properly set.
Here is an example of how I am using it. If ASP.NET validation is successful, I disable the button, otherwise the button remains enabled and the validation summary is displayed to the user. The OnClientClick is from a ASP:Button control.
OnClientClick="javascript:Page_ClientValidate(); if (Page_IsValid==true) { this.disabled=true; }"