HTML/CSS customisation in ALUI 6.1 with Publisher 6.4

Hi,
I'm extremely new to BEA products so apologies upfront for my lack of knowledge. I've read through lots and lots of documentation but what I'm really lacking is practical examples.
I'm trying to implement a new look and feel which requires changing both HTML and CSS. My first task is to change the core site header and footer. In truth, I have no idea where to start. My instinct is to try and alter the header/footer for the Default Experience definition, but is this possible? Could anyone let me know the steps to take to achieve this or to documentation explaining it?
I'm assuming that once the default experience definition is altered then it'll apply site-wide, is this correct? Or would I need a custom experience definition for this? Is it then possible to apply this site-wide?
In terms of portlets I plan on using custom html in the presentation template through Publisher so should be able to comfortably change them, but that's a hurdle for later.
Unfortunately I have little control over the system installation so an upgrade is not possible.
Any help on the above would be very vey appreciated!
Kind regards,
James.

Michael-
Thank you for contacting National Instruments.  This is a known issue in LabVIEW 8.6.1 that was fixed in LabVIEW 2009.  However, you cannot use the RGT 1.1.4 with LabVIEW 2009 or 2009 SP1.  You will need to install the toolkit version for each of those versions of LabVIEW.  You can get these from www.ni.com/src as long as you have an active contract for SSP.  I would recommend downloading the newer version of this toolkit from this website and recreate your EXE files.  This should fix your issue. 
Prior to LabVIEW 2009, you will need to include several *.ctl files and *.lvclass files in your project and include them as source files.  This is outlined in the Knowledge Base Article below. 
KnowledgeBase  4TEK2GXK: Building an EXE in LabVIEW 8.6 and Later Using the Report Generation Toolkit
http://digital.ni.com/public.nsf/allkb/2AE85CF95217E60786257540000D818C?OpenDocument
Regards,
Mike S
NI AE

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    Unfortunately i've never really figuerd out all that div-floating margin-and-padding-overlaping css mambo jumbo
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