Both. To change the font styles and table styles, you will need to edit the .css. To edit look of tables and placement of items in a page, then you will need to edit the templates.
If you want to edit things like how categories and links are listed, you have to edit the site_html_templates.pl file. There have been tons of Threads even in the past week or so discussing how to edit how the categories appear. Search this forum for keywords relating to editing the site_html_templates.pl file.
Regards,
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Eliot Lee
Founder and Editor
Anthro TECH, L.L.C
http://www.anthrotech.com/
info@anthrotech.com
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Coconino Community College
http://www.coco.cc.az.us/
Web Technology
Coordinator
elee@coco.cc.az.us