sccm is horrible when it comes to the boot files..
the easiest method to do x86 and x64 images is to make two different uknown collection
unknown x64 collection
unknown x32 collection
then you set the query as follows for each collection
select SMS_R_UNKNOWNSYSTEM.ResourceID,SMS_R_UNKNOWNSYSTEM.ResourceType,SMS_R_UNKNOWNSYSTEM.Name,SMS_R_UNKNOWNSYSTEM.Name,SMS_R_UNKNOWNSYSTEM.Name from SMS_R_UnknownSystem where Decommissioned = "0" and Name LIKE "%x86%"
and then for x64
select SMS_R_UNKNOWNSYSTEM.ResourceID,SMS_R_UNKNOWNSYSTEM.ResourceType,SMS_R_UNKNOWNSYSTEM.Name,SMS_R_UNKNOWNSYSTEM.Name,SMS_R_UNKNOWNSYSTEM.Name from SMS_R_UnknownSystem where Decommissioned = "0" and Name LIKE "%x64%"
once you do that.. you then advertise your x86 Task sequence and your x64 task sequence to the appropriate collection
and you now have where it will boot the correct boot image
the problem is that sccm cannot have both assigned to the same collection