I've used various tools to assist in this process but usually revert back to a blank sheet of paper. Layouts should be simple and clear. Try to split your form into sections with appropriate subheadings. This will help the user understand what is being requested. It will also encourage you to place data entries in a logical sequence, which is often what a user expects.
Prototypes are very helpful during the design process.
After you've decided on layout, present it to your customer. Hard copy is acceptable, but a simple prototype can usually be put together quickly. Explain that your goal is to settle on a layout early in the development cycle so that you may apply it throughout the project. Finally, do a little surfing. Examine how other sites present forms.