Did you use the 'reassign base address' menu item? It should move the addresses around to avoid clash between peripherals. Just ensure that both s1 and s2 stay at the same address (if they change, you can put them back to a fixed address and click on the lock next to it, to prevent the 'reassign base address' option to change them).
As for the ipport.h modifications, I don't remember the exact procedure, as it was made a long time ago, but it should be explained in the application note. I think there is just a define to add or to uncomment somewhere to tell the driver to use a specific address instead of allocating the packet memory through malloc().