I believe it defines the part of the page to be used for text columns. Here's an example of its use to create 2 column and 3 column layouts:
twoColumn:
frames: []
[0cm, 0cm, 49%, 100%]
[51%, 0cm, 49%, 100%]
showHeader : true
showFooter : true
threeColumn:
frames: []
[2%, 0cm, 29.333%, 100%]
[35.333%, 0cm, 29.333%, 100%]
[68.666%, 0cm, 29.333%, 100%]
showHeader : true
showFooter : true
Here's a document where I did what it sounds like you're trying to do (have the first page print the header/footer, and subsequent pages omit them). I obfuscated the text, but you can see that the first pages has a header (the line with the logo)
The next page does not print the header.
To my eye, it does not look unbalanced to have the same top margin in both cases... but then, our header is not too large.