You normally use any ports 1 through 4. Depends on how your using it though.
If you want to add the ability for wireless computers to access your BEFSR41 router, which is attached to the Internet, you would plug it into any port 1 to 4, just like you would a computer. Then clients (Laptops, etc) will be able to connect through it as a wireless access point. (You must use the cdrom on the wap11 to get started Then, despite the documentation, http over to the IP address you set it to to complete the setup.)
If you want to create a bridge from one group of computers to another, say you have a cluster of a PC, Xbox, laptop in one room connected together with a BEFSR41, and you want to connect to that WRT54GS (or whichever router) a few rooms away, then yes, you CAN connect it to the WAN port AFTER you have gone through the setup on a regular port 1-4. However I should warn this is a painful setup process, as you are creating a second subnet. Unless you are advanced enough to understand what this means - 192.168.1.200/255.255.255.240 I would avoid this approach. It would be much simpler in this scenario to ditch the BEFSR41 and put in a 4 port switch. Then setup your WAP11 as a wireless bridge.
Mine is vs 2, wap11 is 2.8. Mine has an uplink port, and it is the same as port 1 except it has the crossover wired internally for connecting the router to a second hub or switch. If you need an "uplink" port just use a crossover cable instead.