We already have GAL synchronization setup between two AD\Exchange forests using FIM 2010 R2. What we want is to configure Management Agents to put contact objects from specific OU into target specific OU, for example users from DOMAINa/Resursser/Users/Shared Accounts 
should be synchonized and put into DOMAINb/domainaGroups/Shared Accounts
And there is a few pairs of such OUs. Should we configure separate Management Agent in FIM for each pair or is there any way to configure it in one Management Agent?
As You can see on below screen it is impossible to select two containers as target container



You can do it one pair of Management agents by modifying the Galsync.dll code.

If you create multiple GalSync Management Agents with the default code it will take the info from one MA and try and provision a contact to each other GalSync MA, which if you have more than one Galsync MA pointing to the same forest would result in duplicate contacts.