If you are not going to use the MVC Framework (http://www.asp.net/mvc) I would use the MVP model instead. WebForms by themselves are not MVC friendly.
Now, if you want to load a page inside of another page you use an IFrame to do that.
If you want to load a user control onto you page, you can actually just drop the control from the toolbox onto your form.
But you really should get a web development book, or go thru the samples on the asp.net web site.
EDIT: it is not easy to call JavaScript from the server side. But you can use JavaScript to call a web service which could be on your server. The JavaScript could run as the page loads.
EDIT 2: Another item that I have seen confuse desktop developers: how to navigate. And I think that might be giving you some trouble here as well.
The link, all by itself will tell the browser to redirect to another page. You don't want to have to go back to the server for that. It isn't needed. The link needs another attribute: target="_blank" and the next page will appear in a popup dialog. You pass data to the popup via query string parameters. Else you can "save" data into session as well.
Note: the entire browser popup model is broken. Between tabbed browsers and popup blockers you will have trouble. Best if you can use normal browser navigate and drop the entire popup idea entirely. UI paradigms you use on desktop do not always work on web.