Here's my suggestion for best practice for making changes to the Portal. The idea is to basically leave the standard Microsoft SharePoint files alone, so that any changes we make can be easily undone, and if a service pack or fix is released, then it's got less chance of affecting our changes made.
To customize the Portal, first, we need to create a new folder called company_name under:
C:\Program Files\Common Files\Microsoft Shared\web server extensions\60\TEMPLATES\LAYOUTS\1033\
Under this folder, create the following folders to store CSS, image files and alike:
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CSS
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Images
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Scripts
Create a new CSS file under the CSS folder called company_name.css.
On the Portal, then go to Site Settings > Change portal site properties and SharePoint site creation settings.
From here you may want to insert the companies logo (or a banner image) that is stored in the images folder we created above.
You can also now insert the reference to the new CSS file, such as:
/_layouts/1033/company_name/CSS/company_name.css
Copy the contents of SPS.css into company_name.css and make the appropriate changes to that CSS file. It's important to copy the contents of the original CSS file as this makes the editing of our company_name.css file much easier to get our desired effects.