Restoring System Databases on Availability Group Replicas in SQL Server 2014

My question is: - Do i have to schedule the jobs at primary replica and then disable them until fail-over occurs and then manually enable jobs or what is the best way to deal with these please?

No, you should just add a check with the new function sys.fn_hadr_backup_is_preferred_replica

if sys.fn_hadr_backup_is_preferred_replica('your db name') <> 1
begin
    print 'This is not preferred backup replica .....'
        -- If this is not the preferred replica, exit (without error).
end
else
begin
    print 'This is the preferred replica .. continue with backup'
        -- If this is the preferred replica, continue to do the backup.
        -- here goes the backup command .....
end

Alternatively, you can use SQL Server Maintenance Solution - by Ola hallengren which supports AlwaysON as well.

You can setup 2 different availability groups and add databases accordingly, so that way you can manage it separately.