You can customise a Transaction Form PDF Layout (go to Customisation > Forms > Transaction Form PDF Layouts). Next to the Transaction type you want to customise, simply press the "Customise" or "Edit" link. This provides fairly rudimentary functionality.
If you really want to structure your Invoices etc. to your own look and feel, I'd suggest using Advanced PDF/HTML Templates. Read this to enable it in your account if that's not already done. Once you have the functionality, read something like this and this to get you started.
Hope that helps get you started at least.
Cheers,
Kirk.