After you select ASIO and close the dialog box, the profiler will come up. Cancel it, the wave profiler should have no effect when using the ASIO driver as far as I know, only when using MMC/WDM drivers. If you want to adjust the audio settings for an ASIO driver re-open the Audio Options after cancelling the profiler and click on the ASIO Panel button.
One suggestion - when switching between the two cards, disable the other. If you want to use ASIO for the Emu, go to the Audio Options>Driver tab and disable the onboard sound (choosing ASIO should disable it automatically, but, to be on the safe side...). When using the onboard sound disable the Emu in the Driver tab (if it even shows up; if it is not plugged in it likely does not appear). Try selecting the WDM driver for the onboard sound instead of MMC, if possible, and then let the profiler run if necessary (I usually click cancel and skip it as it is usually not necessary). If you have not used the WDM drivers before you likely have to let the profiler run. If both devices are not running you should not have the profiler stall. Hopefully.
I switch between USB and onboard sound all the time with no trouble using this approach. Once the profiler has run once on any card you generally never need to run it again unless you add a new audio interface to the system, Sonar retains the previous settings from when the soundcard/interface was last used.