If you use Protection Manager, the relations will be managed bij Protection Manager and no entry will be added to the snapmirror.conf.
What you can do is import the entries of the snapmirror .conf in Protection Manager.
Schedules will be managed by Protection Manager.
This is what I do:
Create volumes and restrict them on destination.
Create manual snapmirrors by CLI on destination (snapmirror initialize -S source_filer:volume dest_filer:volume
Add entries to snapmirror.conf without schedule( 5 time a minus sign ( -) after the relation you created.
Update the systems in Protection Manager(DOS box, enter ' dfm host list' , get the PM ID's of your systems, enter 'dfm host discover <id's>'
Login in the NMC.
Wait a while, mostly 3 minutes till the snapmirrors are detected and show up in external relations in NMC.
Create mirror policy with schedules you want.
Create dataset, add the volumes from primary to the dataset.
Attach mirror policy you created to the dataset.
Import external relations to dataset.
There are other ways to do this, but this way you are sure that you use the volumes on the destinations and entries in the snapmirror are not affecting Protection Manager.
Also, if you want to use for example autosizing on the destiniation, simply add a resourcepool to the dataset and it will work.
Regards,
Arco