Can I customise the layout of pdf documents with this extension?

Absolutely! It is possible to configure several different layout variations from the backend using the 2 layout options and other custom options (logo placement, margins, integrated labels etc).

From Pdf Customiser version 2.0 onwards, further layout customisations can also be achieved by theming the *.phtml files that come with Pdf Customiser. Please note that this is not done via the backend - basic html/Magento theming knowledge is required. Take a look at these Customisation Tips for how-to and ideas.