You can roll your own theme, via here and then in your popup layout.cshtml
page you can code it that
<head>
<meta charset="utf-8" />
<title>@ViewBag.Title - My ASP.NET MVC Application</title>
<link href="~/favicon.ico" rel="shortcut icon" type="image/x-icon" />
<meta name="viewport" content="width=device-width" />
@Styles.Render("~/Content/css")
@Scripts.Render("~/bundles/modernizr")
if (!string.isNullOrEmpty(Reuqest.QueryString["useCSS"])
{
@Styles.Render("~/Content/css/"+Reuqest.QueryString["useCSS"])
}
</head>
but as you have not provided any code, project layout, description, etc. i am only assuming you mean a full popup window and not just a jquery.ui.dialog object.
EDIT
this solution requires that you create the bundler methods for the new theme.
bundles.Add(new StyleBundle("~/Content/themes/base/css/themeName").Include(
"~/Content/themes/themeName/jquery.ui.core.css",
"~/Content/themes/themeName/jquery.ui.resizable.css",
"~/Content/themes/themeName/jquery.ui.selectable.css",
"~/Content/themes/themeName/jquery.ui.accordion.css",
"~/Content/themes/themeName/jquery.ui.autocomplete.css",
"~/Content/themes/themeName/jquery.ui.button.css",
"~/Content/themes/themeName/jquery.ui.dialog.css",
"~/Content/themes/themeName/jquery.ui.slider.css",
"~/Content/themes/themeName/jquery.ui.tabs.css",
"~/Content/themes/themeName/jquery.ui.datepicker.css",
"~/Content/themes/themeName/jquery.ui.progressbar.css",
"~/Content/themes/themeName/jquery.ui.theme.css"));