Relationship: It's complicated.... Embedding inside a frame + other issues.

[CzarinaOz]

I am trying to create a website for my son's college club sport.. the college is into some sort of "Affirmative Action" so that one web page is not better than another.. so we have to go through their "templates" and "CleanSlate" - which totally stinks. and I am against it. I made my own website in Xara Designer Pro..
Through playing inside the CleanSlate software, I can change most of the elements, but I must keep the "<header> and <footer> of the web page template, so they don't complain, and the only way I can do that, without being a real html jockey (so I don't knock out their editing program by accident - *already happened), is to use one of the "containers" they supply for Media, that give option to include html code.
The "files upload" in CleanSlate will NOT read an "html" file, ....but will read all other files contained in the exported html folder from Xara (png, css, , txt, js, jpg, etc.) that I upload.
Here is my problem:
If I copy/paste the entire webpage's code into the frame/container, besides losing my awesome Layers, I lose the <footer> behind a large jpg at the top of my Xara web page - it is no longer at the bottom.. I have no idea what I need to remove from my code to keep it in... I would like to be able to keep my web animations, if at all possible.
Any ideas? I will try anything! iframes, inside an iframe.. placeholders... whatever I can to make this happen (need to "sock-it-to-the-man")
Also, if you need better explanation just look at this sadness https://womensrugbyclub.orgs.wvu.edu/home
.. that is an example of the boring crap we are talking about here.

Thanks,
Alice