Hi
you need to follow below steps.
1) install agents on all application server, for this action account need to have local admin rights.
2) enable agent proxy for each server
3) download required application mp and documents.
4) create required runas accounts and distribute accounts to required servers as per Mp documents.
5) import application mp to scom dev server and disable all recovery and set threshold as suggested by application team.
6) export mp from dev and import the mp in prod.
refer below link for more information
http://social.technet.microsoft.com/wiki/contents/articles/20796.the-system-center-2012-r2-operations-manager-survival-guide.aspx
Regards