Yes, you can add Worship Beats patches to a Song Specific Patch inside Sunday Keys as long as you are using MainStage 3.4.3 or newer.
First, make sure the Song Specific Patch is above the Worship Beats patch in the Patch List before you choose "Create New Patch From Selection" in the Settings cog. This will ensure that Easy Transpose continues to work as expected.
Second, reset the Tempo and Time Signature settings in the Patch Attributes tab of the Inspector.
Finally, consider a general volume balance between the SSP and the Worship Beats channel strip. You may need to change the levels of some of the channel strips of the SSP in order to hear the Worship Beats at the loudest point in the SSP. They can do this by going into the Gain plugins on each of the channel strips, or by adjusting the volume faders, but keep in mind that those volume faders will return to 0 if the patch is left before saving.