Hi Vasy,
you can try this way:
Create another 'EmbedChannel.ascx'(you only need to copy the code)
when you need cutechat alone,please use the 'EmbedChannel.ascx' which not comment this code
when you nedd cutechat and messenger use in one page,please use the 'EmbedChannel.ascx' which comment this code
Regards,
Ken