The phrase "to agree a procedure" means to come to a mutual understanding and acceptance of how something should be done or accomplished. Full definition
Special meeting 13 May 2015 This was a special meeting, called to agree procedures for choosing the next leader and deputy leader. (leftfutures.org)
You exercised your mind in the same way as you exercised your body: following agreed procedures that shaped you as a useful and responsible member of society. (firstthings.com)
Sometimes one has to deviate from a preliminary agreed procedure to achieve the most beneficial arrangement, which commonly is determined along with negotiations — even at a very advanced stage. (lawyer-monthly.com)