I created a homepage layout using Panels 3, mostly of blocks created by Views.
Now I'd like to apply the visual look and feel as it was designed & sliced. Panels adds an serious amount of divs to its markup. I dont necessarily need to remove this but I do need to add certain classes, id's and change some of the tags used in its markup.
What is the best way to go about this?
It depends what part of the html you what to change, where you should do it. There are two places to do this, either the templates used, where you can create your own with the markup as you please. You could also overwrite the theme functions that panel use and create your custom markup there.
Edit: The templates are located at panels/plugins/layouts. These are the templates for the page layout, printing the different regions on a panel. The other templates that are used comes from different modules depending on what you put into the panel page. So views in a panel will use the views templates ect. However this is also printed through the panel theme functions, theme_panel_pane in particular if I remember correctly. So there are some possibilities, but again, where to do your overwrite depends on what exactly you want to change.
stef, you might want to read this book: Styling & Theming Panels 3 for Drupal