Hi Spt2170,
I am not sure if I completely understand your question.
I did not have a chance to test SharePoint 2010 yet so I can only try to answer your questions based on my experience with WSS 3.
On WSS 3 we derived a custom master page as the default one was rendered in quirks mode (no DOCTYPE was specified). You can see if the browser renders your Intranet page in standard or quirks mode by pressing F12 in Internet Explorer 8 on your homepage.
With the MOSS page being rendered in standard mode we use jQuery for the modal dialog pop ups.
Take a look here for a demo dialog and see if this fits your requirements:
http://jqueryui.com/demos/dialog/#modal
To add jQuery you can add the jQuery script to your masterpage and then call the popup like this by modifying one of the SharePoint pages through SharePoint designer:
$("#dialog-modal").dialog({
height: 140,
modal: true
});
If your page renders in quirks mode and you do not want to change the rendering you can still use jQuery and the impromptu plug-in from here:
http://trentrichardson.com/Impromptu/index.php
Kind regards,
Mathias