Assuming this is just from one site to another it should be pretty straight forward. The GRE Tunnel (in this case) will act just like any other interface you would enable IPX on. We had a similiar situation we fixed with Tunnels across our IP only core. The complexity grows if you want to start linking multiple sites together. At that point you need to add a tunnel for each site to every other site (full mesh). This can get very complex very quickly.
Here is an example of what your Tunnel interface may look like. We tweaked the IPX timers to limit the IPX traffic traversing the IP core between sites. Depending on your situation this may or may not be helpful.
Interface Tunnel<#>
no ip address
ipx delay 1
ipx network
ipx output-rip-delay 1000
ipx output-sap-delay 1000
ipx update interval rip 1200
ipx update interval sap 1200
tunnel source
tunnel destination
Obviously you will need to enable IPX on the router in question and the appropriate interfaces in your lan.
