I guess you would load your flash object code in a new default.aspx, so that it's just the flash intro, and create a new page that is your main page, or just rename the current default page, and create the new page.
And alter the flash swf source code to redirect to the new main page when done playing, perhaps add a skip button to do a redirect.
[EDIT]
Didn't know that. I can't help you with that. I use flash swf files that I wrote from scratch, which include loaders, or flashvars, in which I call a swf program, that loads whatevers in the flash var.
This is the basic framework for a flash object that I use, for a swf written in Flash CS3, or codebase 9. It uses the names, to identify the objects, so you can find the objects in Javascript and destroy it.
Notes:
Remove the flash vars element, for basic SWF files.
To size the object, size it to the original size of the SWF file,
You can place the object in a container div tags, and use css to align the object horizontal and vertical
The object is for IE, and the embed is for firefox, so if one works but not the others, then there is a mistake in the object for IE or embed for firefox.
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" width="320" height="240" id="flv_Player1" name="flv_Player1">
<param name="movie" value="/Movies/players/flv_stream_player.swf" />
<param name="allowfullscreen" value="false" />
<param name="allowscriptaccess" value="always" />
<param name="autostart" value="true" />
<param name="flashvars" value="moviefile=/Movies/MovieFiles/temp/03-440SB36CuttingGlass.flv&autoplay=1&playerskin=/Movies/players/SkinUnderAll.swf&videowidth=320&videoheight=240&playerwidth=240&playerheight=320" />
<param name="wmode" value="transparent" />
<embed id="flv_Player2"
name="flv_Player2"
src="/Movies/players/flv_stream_player.swf"
width="320"
height="240"
allowscriptaccess="always"
autostart="true"
allowfullscreen="false"
wmode="transparent"
flashvars="moviefile=/Movies/MovieFiles/temp/03-440SB36CuttingGlass.flv&autoplay=1&playerskin=/Movies/players/SkinUnderAll.swf&videowidth=320&videoheight=240&playerwidth=240&playerheight=320"
/>
</object>