I have been doing some work with Websphere My personal preference is to not install a profile at this time, but rather install WAS and any required fixes, and then come back and use the Profile Management Tool to create the profile I need for that particular instance. This is also helpful if you clone machines and use them for different purposes (ie deployment manager or Application Server). In the 32 Bit version of WAS you can use the Graphical Profile Management (tutorial) tool to create profiles. The Graphical Profile Management tool is not available in the 64 bit versions of Domino (except for Linux on zSeries which I am sure will please Bill) From the WAS 7.0 Infocenter
You cannot use the Profile Management Tool to create profiles for WebSphere Application Server installations on 64-bit architectures except on the Linux for zSeries platform. However, you can use the Profile Management Tool on other 64–bit architectures if you use a WebSphere Application Server 32–bit installation.
I had forgotten about this, so I spent a few puzzled minutes looking for the menu option for the Profile Management tool, when I finally remembered it did not exist for 64 Bit. If you are on a 64 Bit install of WAS you have to use the manageprofiles command located in the<WAS_ROOT>bin directory. You can find the command line options here.