Debugging is easy if you have set up correct Server Runtime for your Seam Web Project.
Use right mouse button click on your Seam project and select Properties. Properties dialog is shown and there should be Server settings in list of available items.
If you can't see it there, you have to set up/add to your project Web Tools Project facet. Just use right mouse button click on your Seam project and select Configure - Add JSF Capabilities and in following wizard set up correct Server Runtime, which you would like to use for debugging.
Then just set breakpoints in your java classes and click right mouse button on a class and choose Debug As - Debug on Server. It should deploy your project on configured Server Runtime and launch Debug Perspective if you want.